diff --git a/README.md b/README.md index 0c40fd4..1afba76 100644 --- a/README.md +++ b/README.md @@ -40,6 +40,7 @@ TRUST4 is also available form [Bioconda](https://anaconda.org/bioconda/trust4). -o STRING: prefix of output files. (default: inferred from file prefix) --od STRING: the directory for output files. (default: ./) -t INT: number of threads (default: 1) + -k INT: the starting k-mer size for indexing contigs (default: 9) --barcode STRING: if -b, bam field for barcode; if -1 -2/-u, file containing barcodes (defaul: not used) --barcodeRange INT INT CHAR: start, end(-1 for lenght-1), strand in a barcode is the true barcode (default: 0 -1 +) --barcodeWhitelist STRING: path to the barcode whitelist (default: not used) diff --git a/example/TRUST_example_airr.tsv b/example/TRUST_example_airr.tsv index 2719f67..213b545 100644 --- a/example/TRUST_example_airr.tsv +++ b/example/TRUST_example_airr.tsv @@ -1,18 +1,18 @@ sequence_id sequence rev_comp productive v_call d_call j_call c_call sequence_alignment germline_alignment cdr1 cdr2 junction junction_aa v_cigar d_cigar j_cigar v_identity j_identity cell_id complete_vdj consensus_count -assemble1_0 GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCC F F IGHV1-3*01 IGHD1-26*01 IGHJ6*04 GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTAC---ATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAG-CTACTACTACTACTACGGTATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG 17N278M111S1N 308S8N5M1D7M68S 315S2N15M3I43M16S 100.00 92.44 F 4 -assemble2_0 CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGGGAGTGCATCCGCCC F F IGHV4-61*01 IGHD2-2*01 IGHJ3*02 CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG GGTGGCTCCGTCAGCAGTGGTAGTTACTAC ATCTATTACAGTGGGAGCACC TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG 61N235M109S3N 248S3N25M71S3N 281S3N47M16S 100.00 100.00 F 3 -assemble3_0 AGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGC F F IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 AGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAA---CTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA AGTCTGGGGGAGGCGTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGATTCACCTTCAGTAGCTATGGC ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG 16N277M98S3N 285S10N14M76S4N 304S3N1M3I55M15S 95.29 97.39 F 2 +assemble1_0 GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCC F F IGHV1-3*01 IGHD1-26*01 IGHJ6*04 GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTAC---ATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG GTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAG-CTACTACTACTACTACGGTATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG 17N278M111S1N 308S8N5M1D7M68S 315S2N15M3I43M16S 100.00 92.44 F 8 +assemble2_0 CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGGGAGTGCATCCGCCC F F IGHV4-61*01 IGHD2-2*01 IGHJ3*02 CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG CCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG GGTGGCTCCGTCAGCAGTGGTAGTTACTAC ATCTATTACAGTGGGAGCACC TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG 61N235M109S3N 248S3N25M71S3N 281S3N47M16S 100.00 100.00 F 6 +assemble3_0 AGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGC F F IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 AGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAA---CTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA AGTCTGGGGGAGGCGTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGATTCACCTTCAGTAGCTATGGC ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG 16N277M98S3N 285S10N14M76S4N 304S3N1M3I55M15S 95.29 97.39 F 3 assemble5_0 GTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATAAACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAG F F IGHV3-11*01 IGHD6-19*01 IGHJ4*02 IGHM GTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATAAACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GGATTCACCTTCAGTGACTACTAC ATTAGTAGTAGTGGTAGTACCATA TGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGG 64N232M129S 242S6N13M106S2N 273S5N43M45S 99.14 100.00 F 3 assemble7_0 TGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCTGGGTCACCATGACCAGGGACACGTCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCT F F IGHV1-2*04 IGHD4-17*01 IGHJ4*02 IGHM TGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCTGGGTCACCATGACCAGGGACACGTCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG TGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCTGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GGATACACCTTCACCGGCTACTAT ATCAACCCTAACAGTGGTGGCACA TGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGG 41N255M110S 280S2N14M71S 280S48M37S 98.04 100.00 F 1 assemble9_0 TGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCTTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCC F T IGHV1-69*01 IGHD2-8*02 IGHJ6*04 IGHM TGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCTTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTAC---ATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG TGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTATACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACGGTATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG GGAGGCACCTTCAGCAGCTATGCT ATCATCCTTATCTTTGGTACAGCA TGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACATGGACGTCTGG CASNAGLYWWCMLNNGFRSRGRSYYYYYMDVW 52N241M141S3N 250S5N25M107S1N 301S1N16M3I43M22S 99.59 92.56 F 2 -assemble10_0 CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATTGCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGGA F F IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATTGCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCAT---TAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGT---ACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGATTCACCTTCAGTAGCTATTGC ATTAGTAGTAGTAGTACCATA GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG 36N116M3I130M192S11N 249S25M164S6N 285S2N1M3I56M96S 97.96 97.44 F 3 +assemble10_0 CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATTGCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGGA F F IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATTGCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCAT---TAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGT---ACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA CAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACGGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGATTCACCTTCAGTAGCTATTGC ATTAGTAGTAGTAGTACCATA GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG 36N116M3I130M192S11N 249S25M164S6N 285S2N1M3I56M96S 97.96 97.44 F 4 assemble11_0 GGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAG F F IGHV5-51*01 IGHD1-26*01 IGHJ3*02 IGHM GGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG GGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACAAGTGGGAGCTACCCTCATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG ATCTATCCTGGTGACTCTGATACC TGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGG 139N157M160S 157S5N12M148S3N 174S50M93S 100.00 100.00 F 3 assemble12_0 GGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTC F F IGHV3-69-1*01 IGHD2-15*01 IGHJ5*02 GGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTC GGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTC ATTAGTAGTAGTAGTACCATA TGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGG 124N166M96S3N 183S1N29M50S1N 229S5N33M13N 100.00 100.00 F 3 assemble13_0 TACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACTGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGG F F IGHV1-18*01 IGHD2-15*01 IGHJ6*04 IGHM TACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTAC---ATGGACGTCTGGGGCAAAGGGACCACGGTCACTGTCTCCTCAG TACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTGGTGGTAGCTG-CTACTACTACTACTACGGTATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG TGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTACATGGACGTCTGG 237N57M210S2N 94S5N19M1D5M148S2N 115S2N15M3I43M94S 100.00 90.76 F 3 assemble15_0 ATTCGCCTTCAGTAGCTATGCTCTGCACTGGGTTCGCCGGGCTCCAGGGAAGGGTCTGGAGTGGGTATCAGCTATTGGTACTGGTGGTGATACATACTATGCAGACTCCGTGATGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAAGTCCTTGTATCTTCATATGAACAGCCTGATAGCTGAGGACATGGCTGTGTATTATTGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGC F F IGHV3-47*01 IGHD2-2*02 IGHJ4*02 IGHM ATTCGCCTTCAGTAGCTATGCTCTGCACTGGGTTCGCCGGGCTCCAGGGAAGGGTCTGGAGTGGGTATCAGCTATTGGTACTGGTGGTGATACATACTATGCAGACTCCGTGATGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAAGTCCTTGTATCTTCATATGAACAGCCTGATAGCTGAGGACATGGCTGTGTATTATTGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ATTCGCCTTCAGTAGCTATGCTCTGCACTGGGTTCGCCGGGCTCCAGGGAAGGGTCTGGAGTGGGTATCAGCTATTGGTACTGGTGGTGATACATACTATGCAGACTCCGTGATGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAAGTCCTTGTATCTTCATATGAACAGCCTGATAGCTGAGGACATGGCTGTGTATTATTGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ATTGGTACTGGTGGTGATACA TGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGG 77N214M158S 225S15N15M132S1N 237S2N46M89S 100.00 100.00 F 2 assemble17_0 GACTACTACATGAGCTGGGTCCGCCAGGCTCCCGGGAAGGGGCTGGAGTGGGTAGGTTTCATTAGAAACAAAGCTAATGGTGGGACAACAGAATAGACCACGTCTGTGAAAGGCAGATTCACAATCTCAAGAGATGATTCCAAAAGCATCACCTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGGGGCCAGGGAACCCTGGTCAC F T IGHV3-71*01 IGHD6-19*01 IGHJ5*02 GACTACTACATGAGCTGGGTCCGCCAGGCTCCCGGGAAGGGGCTGGAGTGGGTAGGTTTCATTAGAAACAAAGCTAATGGTGGGACAACAGAATAGACCACGTCTGTGAAAGGCAGATTCACAATCTCAAGAGATGATTCCAAAAGCATCACCTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGGGGCCAGGGAACCCTGGTCAC GACTACTACATGAGCTGGGTCCGCCAGGCTCCCGGGAAGGGGCTGGAGTGGGTAGGTTTCATTAGAAACAAAGCTAATGGTGGGACAACAGAATAGACCACGTCTGTGAAAGGCAGATTCACAATCTCAAGAGATGATTCCAAAAGCATCACCTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGG------TTCGACCCCTGGGGCCAGGGAACCCTGGTCAC ATTAGAAACAAAGCTAATGGTGGGACAACA TGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGG CARDLGRRYSSGWFCFDPW 90N212M66S 223S1N18M37S2N 236S4N4M6D32M11N 100.00 92.31 F 1 assemble19_0 CAGCTATTGGTACTGCTGGTGACACATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAG F T IGHV3-13*01 IGHD2-2*01 IGHJ6*02 CAGCTATTGGTACTGCTGGTGACACATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTTATTGTAGTAGTACCAGCTGCTAT---TACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA CAGCTATTGGTACTGCTGGTGACACATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA ATTGGTACTGCTGGTGACACA TGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACGGTATGGACGTCTGG CYCSSTSCYYYYYGMDVW 145N140M87S8N 140S4N24M63S3N 162S2M3I57M6S 100.00 97.52 F 2 -assemble21_0 CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCC F F IGHV4-61*01 IGHD2-2*01 IGHJ4*02 IGHM CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ATCTATTACAGTGGGAGCACC TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG 123N176M115S 188S7N22M81S2N 228S7N41M22S 100.00 100.00 F 3 +assemble21_0 CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCC F F IGHV4-61*01 IGHD2-2*01 IGHJ4*02 IGHM CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG CCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ATCTATTACAGTGGGAGCACC TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG 123N176M115S 188S7N22M81S2N 228S7N41M22S 100.00 100.00 F 5 assemble25_0 GCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTAACCATCTCCAGAGACAACGCCAAGAACNNNNNNNAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGGACTT F F IGHV3-74*01 IGHD2-15*01 IGHJ5*02 IGHM GCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTAACCATCTCCAGAGACAACGCCAAGAAC------NNNNNNNAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ATTAATAGTGATGGGAGTAGCACA TGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGG 131N100M6I59M187S 177S5N22M147S4N 201S4N47M98S 93.21 100.00 F 3 assemble26_0 ACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGGACTTC F F IGHV3-11*04 IGHD2-15*01 IGHJ4*02 IGHM ACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG ACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG TGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGG 229N64M186S3N 73S1N27M150S3N 110S7N41M99S 100.00 100.00 F 3 assemble27_0 CCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATCATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGGGGCCAGGGAACCCTGGTCNNNNNNNCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCACAGG F F IGHV4-38-2*01 IGHD3-22*01 IGHJ4*02 IGHM CCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATCATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGGGGCCAGGGAACCCTGGTC CCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATCATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGGGGCCAGGGAACCCTGGTC ATCTATCATAGTGGGAGCACC TGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGG 121N172M172S1N 183S8N16M145S7N 206S4N31M107S13N 97.65 100.00 F 2 @@ -21,7 +21,7 @@ assemble30_0 CTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATAGGGAGTTGT assemble31_0 TGCAAATGAACAGCCTGAGAGCCGAGCACACGGCCGTATATTACTGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATCCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGCCTCGCA F T IGHV3-23*01 IGHD2-2*01 IGHJ4*02 IGHM TGCAAATGAACAGCCTGAGAGCCGAGCACACGGCCGTATATTACTGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATCCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG TGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATGCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG TGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATCCCCTTTGACTACTGG CAKDVASTRALPKPPVVVVPAAIPFDYW 241N55M194S 90S6N25M134S 115S4N44M90S 98.18 100.00 F 2 assemble33_0 AAATGGACAGTCTGAAAGCTAAGGACACGGCCATGTATTACTGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGCGTGGCCGTTGGCTGC F F IGHV3-41*02 IGHD3-10*01 IGHJ3*02 IGHM AAATGGACAGTCTGAAAGCTAAGGACACGGCCATGTATTACTGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG AAATGGACAGTCTGAAAGCTAAGGACACGGCCATGTATTACTGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG TGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGG 244N44M158S6N 50S3N12M140S16N 71S3N47M84S 100.00 100.00 F 2 assemble34_0 CGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCC F T IGHV3-66*01 IGHD2-15*01 IGHJ4*02 IGHM CGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG CGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG TGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGG CARDIVVVVVAATPRAQIYW 229N64M132S 69S6N25M102S 107S11N37M52S 96.83 97.22 F 2 -assemble36_0 GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCAT F F IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCT---ACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG 96N200M119S 219S2N16M84S 251S2N1M3I56M11S 100.00 97.44 F 2 +assemble36_0 GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCAT F F IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCT---ACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA GGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGTAGCACATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG 96N200M119S 219S2N16M84S 251S2N1M3I56M11S 100.00 97.44 F 3 assemble37_0 AGATCTGAAGACACGGCTGTGTATTACTGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCC F F IGHV1-3*01 IGHD6-13*01 IGHJ6*02 IGHM AGATCTGAAGACACGGCTGTGTATTACTGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA AGATCTGAAGACACGGCTGTGTATTACTGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA TGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGG 258N36M141S2N 39S3N18M120S 63S1N61M53S 100.00 95.08 F 3 assemble39_0 GGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGGAGT F F IGHV1-3*01 IGHD1-1*01 IGHJ5*02 GGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GGCCTCAGTGAAGGTTTCCTGCAAGGCTTCTGGATACACCTTCACTAGCTATGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCTTGAGTGGATGGGATGGATCAACGCTGGCAATGGTAACACAAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATCCGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTGTGTATTACTGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGG 44N248M82S4N 271S1N16M43S 273S51M6S 100.00 100.00 F 2 assemble40_0 TGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGAGAGGGATAGCAGTGGCTTGGGTACTACTACTACTACATGGACGTCTGGGGCAAAG F F IGHV5-51*01 IGHD6-19*01 IGHJ6*03 TGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGAGAGGGATAGCAGTGGCTTGGGT---ACTACTACTACTACATGGACGTCTGGGGCAAAG TGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGAGAGGGATAGCAGTGGCTTGGGTACTACTACTACTACTACATGGACGTCTGGGGCAAAG GGATACAGCTTTACCAGCTACTGG ATCTATCCTGGTGACTCTGATACC TGTGCGAGAGAGGGATAGCAGTGGCTTGGGTACTACTACTACTACATGGACGTCTGG 31N263M55S2N 268S4N12M38S5N 284S2N1M3I33M23N 100.00 87.32 F 2 diff --git a/example/TRUST_example_cdr3.out b/example/TRUST_example_cdr3.out index 18d2e9b..8f8afab 100644 --- a/example/TRUST_example_cdr3.out +++ b/example/TRUST_example_cdr3.out @@ -1,13 +1,13 @@ assemble0 0 IGHV5-51*01 * * * GGATACAGCTTTACCAGCTACTGG ATCTATCCTGGTGACTCTGATACC TGTGCGAGACATCTTGGAGATTGTGGTGGTGACTGC 0.00 3.00 0.00 0 -assemble1 0 IGHV1-3*01 IGHD1-26*01 IGHJ6*04 * GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG 1.00 4.00 94.00 0 -assemble2 0 IGHV4-61*01 IGHD2-2*01 IGHJ3*02 * GGTGGCTCCGTCAGCAGTGGTAGTTACTAC ATCTATTACAGTGGGAGCACC TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG 1.00 3.00 100.00 0 -assemble3 0 IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 * GGATTCACCTTCAGTAGCTATGGC ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG 1.00 2.00 93.88 0 +assemble1 0 IGHV1-3*01 IGHD1-26*01 IGHJ6*04 * GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG 1.00 8.00 94.00 0 +assemble2 0 IGHV4-61*01 IGHD2-2*01 IGHJ3*02 * GGTGGCTCCGTCAGCAGTGGTAGTTACTAC ATCTATTACAGTGGGAGCACC TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG 1.00 6.00 100.00 0 +assemble3 0 IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 * GGATTCACCTTCAGTAGCTATGGC ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG 1.00 3.00 93.88 0 assemble4 0 IGHV3-7*03 * * * GGATTCACCTTCAGTAGCTATTGC ATAAAGCAAGATGGAAGTGAGAAA TGTGCGAGAGGGAGATATTGT 0.00 1.00 0.00 0 assemble5 0 IGHV3-11*01 IGHD6-19*01 IGHJ4*02 IGHM GGATTCACCTTCAGTGACTACTAC ATTAGTAGTAGTGGTAGTACCATA TGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGG 1.00 3.00 100.00 0 assemble6 0 IGHV3-23*01 * IGHJ4*02 IGHM GGATTCACCTTTAGCAGCTATGCC ATTAGTGGTAGTGGTGGTAGCACA GCGAAAGCCGCATGACTCACGTACAGTAACTCCACATTTGACTACTGG 0.00 1.00 0.00 0 assemble7 0 IGHV1-2*04 IGHD4-17*01 IGHJ4*02 IGHM GGATACACCTTCACCGGCTACTAT ATCAACCCTAACAGTGGTGGCACA TGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGG 1.00 1.00 95.00 0 assemble9 0 IGHV1-69*01 IGHD2-8*02 IGHJ6*04 IGHM GGAGGCACCTTCAGCAGCTATGCT ATCATCCTTATCTTTGGTACAGCA TGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACATGGACGTCTGG 1.00 2.00 93.55 0 -assemble10 0 IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM GGATTCACCTTCAGTAGCTATTGC ATTAGTAGTAGTAGTACCATA GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG 0.83 3.00 0.00 0 +assemble10 0 IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM GGATTCACCTTCAGTAGCTATTGC ATTAGTAGTAGTAGTACCATA GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG 0.83 4.00 0.00 0 assemble11 0 IGHV5-51*01 IGHD1-26*01 IGHJ3*02 IGHM * ATCTATCCTGGTGACTCTGATACC TGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGG 1.00 3.00 97.50 0 assemble12 0 IGHV3-69-1*01 IGHD2-15*01 IGHJ5*02 * * ATTAGTAGTAGTAGTACCATA TGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGG 1.00 3.00 100.00 0 assemble13 0 IGHV1-18*01 IGHD2-15*01 IGHJ6*04 IGHM * * TGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTACATGGACGTCTGG 1.00 3.00 88.52 0 @@ -15,7 +15,7 @@ assemble15 0 IGHV3-47*01 IGHD2-2*02 IGHJ4*02 IGHM * ATTGGTACTGGTGGTGATACA TGTGCA assemble16 0 * * IGHJ6*02 IGHM * * GGGTATAGCAGTGGCTGGTCCACGTACTACTACGGTATGGACGTCTGG 0.00 1.00 0.00 0 assemble17 0 IGHV3-71*01 IGHD6-19*01 IGHJ5*02 * * ATTAGAAACAAAGCTAATGGTGGGACAACA TGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGG 1.00 1.00 100.00 0 assemble19 0 IGHV3-13*01 IGHD2-2*01 IGHJ6*02 * * ATTGGTACTGCTGGTGACACA TGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACGGTATGGACGTCTGG 1.00 2.00 94.74 0 -assemble21 0 IGHV4-61*01,IGHV4-59*01 IGHD2-2*01 IGHJ4*02 IGHM * ATCTATTACAGTGGGAGCACC TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG 1.00 3.00 100.00 0 +assemble21 0 IGHV4-61*01,IGHV4-59*01 IGHD2-2*01 IGHJ4*02 IGHM * ATCTATTACAGTGGGAGCACC TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG 1.00 5.00 100.00 0 assemble22 0 IGHV3-74*01 * * * GGATTCACCTTCAGTAGCTACTGG ATTAATAGTGATGGGAGTAGCACA TGTGCAAGCATTTGAATATAGCAGCTCGTCATTGTGATAACT 0.00 2.00 0.00 0 assemble24 0 IGHV6-1*01 * * * GGGGACAGTGTCTCTAGCAACAGTGCTGCT ACATACTACAGGTCCAAGTGGTATAAT TGTGCAAGACCTTCCGCATAGCAGTGG 0.00 1.00 0.00 0 assemble25 0 IGHV3-74*01 IGHD2-15*01 IGHJ5*02 IGHM * ATTAATAGTGATGGGAGTAGCACA TGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGG 1.00 3.00 100.00 0 @@ -28,7 +28,7 @@ assemble31 0 IGHV3-23*01 IGHD2-2*01 IGHJ4*02 IGHM * * TGTGCGAAAGACGTTGCAAGCACCAG assemble32 0 IGHV1-3*01 * * * * ATCAACGCTGGCAATGGTAACACA TGTGCGAGAGTAAGAGCCGCTGTCTATTGTAGTAGTACCAGCTGG 0.00 2.00 0.00 0 assemble33 0 IGHV3-41*02 IGHD3-10*01 IGHJ3*02 IGHM * * TGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGG 1.00 2.00 100.00 0 assemble34 0 IGHV3-66*01 IGHD2-15*01 IGHJ4*02 IGHM * * TGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGG 1.00 2.00 100.00 0 -assemble36 0 IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 * * ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG 1.00 2.00 94.55 0 +assemble36 0 IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 * * ATTTATAGCGGTGGTAGTAGCACA TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG 1.00 3.00 94.55 0 assemble37 0 IGHV1-3*01 IGHD6-13*01 IGHJ6*02 IGHM * * TGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGG 1.00 3.00 100.00 0 assemble38 0 IGHV4-59*10 * * * GGTGGCTCCATCAGTAGTTACTAC ATCTATTACAGTGGGAGCACC TGTGCGAGGGGGCGAACG 0.00 1.00 0.00 0 assemble39 0 IGHV1-3*01 IGHD1-1*01 IGHJ5*02 * GGATACACCTTCACTAGCTATGCT ATCAACGCTGGCAATGGTAACACA TGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGG 1.00 2.00 95.12 0 diff --git a/example/TRUST_example_report.tsv b/example/TRUST_example_report.tsv index ae56b8f..da82227 100644 --- a/example/TRUST_example_report.tsv +++ b/example/TRUST_example_report.tsv @@ -1,44 +1,44 @@ #count frequency CDR3nt CDR3aa V D J C cid cid_full_length -4 4.761905e-02 TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD1-26*01 IGHJ6*04 . assemble1 0 -3 3.571429e-02 TGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD6-13*01 IGHJ6*02 IGHM assemble37 0 -3 3.571429e-02 TGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGG out_of_frame IGHV3-69-1*01 IGHD2-15*01 IGHJ5*02 . assemble12 0 -3 3.571429e-02 TGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGG out_of_frame IGHV3-11*01 IGHD6-19*01 IGHJ4*02 IGHM assemble5 0 -3 3.571429e-02 TGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGG out_of_frame IGHV5-51*01 IGHD1-26*01 IGHJ3*02 IGHM assemble11 0 -3 3.571429e-02 TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG out_of_frame IGHV4-61*01 IGHD2-2*01 IGHJ3*02 . assemble2 0 -3 3.571429e-02 GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG GVLRFLEWL_KRGYYYYGMDVW IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM assemble10 0 -3 3.571429e-02 TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG out_of_frame IGHV4-61*01 IGHD2-2*01 IGHJ4*02 IGHM assemble21 0 -3 3.571429e-02 TGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGG out_of_frame IGHV3-11*04 IGHD2-15*01 IGHJ4*02 IGHM assemble26 0 -3 3.571429e-02 TGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-18*01 IGHD2-15*01 IGHJ6*04 IGHM assemble13 0 -3 3.571429e-02 TGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGG CARDVGGVFPL_WW_LLCWFDPW IGHV3-74*01 IGHD2-15*01 IGHJ5*02 IGHM assemble25 0 -2 2.380952e-02 TGTGCGAGAGAGGGATAGCAGTGGCTTGGGTACTACTACTACTACATGGACGTCTGG CAREG_QWLGYYYYYMDVW IGHV5-51*01 IGHD6-19*01 IGHJ6*03 . assemble40 0 -2 2.380952e-02 TGTGTGTCCCTCAGAATTACTATGGTTCAGATTCGAACTCGAAGAACTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-NL1*01 IGHD3-10*01 IGHJ6*04 IGHM assemble28 0 -2 2.380952e-02 TGTGGGGTTCGGGGAGTTAACATCGATAAGAAGTAATACTACTACTACTACGGTATGGACGTCTGG CGVRGVNIDKK_YYYYYGMDVW IGHV3-49*02 IGHD3-10*01 IGHJ6*02 IGHM assemble61 0 -2 2.380952e-02 TGTGCGAGAGTGCAAGTGACCTAATAGCAGTGGCTGGTACGATTCCATACTTTGACTACTGG out_of_frame IGHV1-46*01 IGHD6-19*01 IGHJ4*02 IGHM assemble64 0 -2 2.380952e-02 TGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGG out_of_frame IGHV3-41*02 IGHD3-10*01 IGHJ3*02 IGHM assemble33 0 -2 2.380952e-02 TGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGG out_of_frame IGHV4-38-2*01 IGHD3-22*01 IGHJ4*02 IGHM assemble27 0 -2 2.380952e-02 TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 . assemble3 0 -2 2.380952e-02 TGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACATGGACGTCTGG CASNAGLYWWCMLNNGFRSRGRSYYYYYMDVW IGHV1-69*01 IGHD2-8*02 IGHJ6*04 IGHM assemble9 0 -2 2.380952e-02 TGTGCACGGCACCCGGGTCTGTGCCTAGTATTACTATGGTTCAGGGATACTACTACTACATGGACGTCTGG out_of_frame IGHV2-70*01 IGHD3-10*01 IGHJ6*04 IGHM assemble44 0 -2 2.380952e-02 TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 . assemble36 0 -2 2.380952e-02 TGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATCCCCTTTGACTACTGG CAKDVASTRALPKPPVVVVPAAIPFDYW IGHV3-23*01 IGHD2-2*01 IGHJ4*02 IGHM assemble31 0 -2 2.380952e-02 TGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACGGTATGGACGTCTGG CYCSSTSCYYYYYGMDVW IGHV3-13*01 IGHD2-2*01 IGHJ6*02 . assemble19 0 -2 2.380952e-02 TGTAGTGGTGGTAGCTGCTATAGTAAGTACTACTTTGACGACTGG CSGGSCYSKYYFDDW IGHV3-23*01 IGHD2-15*01 IGHJ4*02 IGHM assemble46 0 -2 2.380952e-02 TGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGG out_of_frame IGHV3-47*01 IGHD2-2*02 IGHJ4*02 IGHM assemble15 0 -2 2.380952e-02 TGTGCGAGAGATAGGGAGTTGTAGTAGTACCAGCTGCTGTCACGGGACTACTACTACTACTACTACATGGACGTCTGG CARDREL__YQLLSRDYYYYYYMDVW IGHV3-11*04 IGHD2-2*01 IGHJ6*04 IGHM assemble30 0 -2 2.380952e-02 TGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGG CARDIVVVVVAATPRAQIYW IGHV3-66*01 IGHD2-15*01 IGHJ4*02 IGHM assemble34 0 -2 2.380952e-02 TGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGG out_of_frame IGHV1-3*01 IGHD1-1*01 IGHJ5*02 . assemble39 0 -2 2.380952e-02 TGTGCGAGAGGCGATACCCGGTATTACGATTTTTGGAGTGGTTATTATCCGCAAAGAGGACCAGGGCAGTCCTACTACTACTACGGTATGGACGTCTGG CARGDTRYYDFWSGYYPQRGPGQSYYYYGMDVW IGHV3-11*04 IGHD3-3*01 IGHJ6*02 IGHM assemble41 0 -1 1.190476e-02 TGTGTGAGAGGGGCCATCCCCTACGGTGAGTAAACACGAATATTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV3-52*01 IGHD4-23*01 IGHJ6*04 IGHM assemble60 0 -1 1.190476e-02 TGTGCGAGAGACCCCTATTACTATGATAGTAGTGGTTATATGCCGTGACCCAGCTCGACCCCTGG out_of_frame IGHV4-61*01 IGHD3-22*01 IGHJ5*02 . assemble79 0 -1 1.190476e-02 TGTGCGAGGACCGGCCCTATAGCAGTGGCTGGTTTCACTAGGTTACTGG out_of_frame IGHV1-46*01 IGHD6-19*01 IGHJ4*02 . assemble77 0 -1 1.190476e-02 TGTGCGAGAGATGAGATTACGATATTTTGACTGGTTATTATCTGACCGAGCTGGTTTTGAGTTCCCTGAAATCCACCTAACCTGCGCAACTACTGG CARDEITIF_LVII_PSWF_VP_NPPNLRNYW IGHV1-3*01 IGHD3-9*01 IGHJ4*02 . assemble57 0 -1 1.190476e-02 TGTGCGAACGGAGGCAGCAGAAAGGTGTCTTGGGATGGTTCGACCCCTGG out_of_frame IGHV3-NL1*01 IGHD3-10*01 IGHJ5*02 . assemble53 0 -1 1.190476e-02 TGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGG out_of_frame IGHV1-2*04 IGHD4-17*01 IGHJ4*02 IGHM assemble7 0 -1 1.190476e-02 TGTGCGAGAGATGGAAGCGGCGTATTACGATTTTTGGAGTGGTTCTTCCGACCATACTACTACTACTACATGGACGTCTGG CARDGSGVLRFLEWFFRPYYYYYMDVW IGHV3-11*04 IGHD3-3*01 IGHJ6*04 IGHM assemble67 0 -1 1.190476e-02 TGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGG CARDLGRRYSSGWFCFDPW IGHV3-71*01 IGHD6-19*01 IGHJ5*02 . assemble17 0 -1 1.190476e-02 TGTGCGAAAGATATACTAGTATGATAGTAGTGGTTATGGGTTCATTGTTTACTACTGG out_of_frame IGHV3-NL1*01 IGHD3-22*01 IGHJ4*02 IGHM assemble75 0 -1 1.190476e-02 TGTGCGAGAGCTGTAACTTATATTGTAGTAGTACCAGCTGCGGGCTGACAGTTTACTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD2-2*01 IGHJ6*02 IGHM assemble50 0 -1 1.190476e-02 TGTGCGAAAGATAGTAGTGGCTACGATTGAATGTTGACTACTGG out_of_frame IGHV3-NL1*01 IGHD5-12*01 IGHJ4*02 . assemble58 0 -1 1.190476e-02 TGTGCGAGAGACCGGCGTTCGTGATACAGCTATGGTTACCGGACACTCCTACTACTACATGGACGTCTGG out_of_frame IGHV1-18*01 IGHD5-18*01 IGHJ6*04 IGHM assemble49 0 -1 1.190476e-02 TGTGCGAGAGATCGGAGATACCCCTTGACAAGGTATAGCAGTGGCTGGTACGAAATTAATGATGCTTTTGATATCTGG CARDRRYPLTRYSSGWYEINDAFDIW IGHV3-11*01 IGHD6-19*01 IGHJ3*02 . assemble69 0 -1 1.190476e-02 TGTGCGAAAGATCTCCCGAACTTATGTATATGTCTGGTGGTTCGACCCCTGG out_of_frame IGHV3-NL1*01 IGHD2-8*02 IGHJ5*02 IGHM assemble56 0 +8 8.333333e-02 TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD1-26*01 IGHJ6*04 . assemble1 0 +6 6.250000e-02 TGTGCGAGGGGGCGAACGATAATATTGTAGTAGTACCAGCTGCTATCTTCCATTTGCTTTTGATATCTGG out_of_frame IGHV4-61*01 IGHD2-2*01 IGHJ3*02 . assemble2 0 +5 5.208333e-02 TGTGCGAGAGATGGTACCCCGGATGTAGTAGTACCAGCTGCTATGTTTCTTAAACCGGTTGTCTGACTACTGG out_of_frame IGHV4-61*01 IGHD2-2*01 IGHJ4*02 IGHM assemble21 0 +4 4.166667e-02 GGGGTATTACGATTTTTGGAGTGGTTATAAAAGCGGGGGTACTACTACTACGGTATGGACGTCTGG GVLRFLEWL_KRGYYYYGMDVW IGHV3-48*04 IGHD3-3*01 IGHJ6*02 IGHM assemble10 0 +3 3.125000e-02 TGTGCGAGACCCTATAGCAGCAGCTGGTACGAAAGTTTACTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD6-13*01 IGHJ6*02 IGHM assemble37 0 +3 3.125000e-02 TGTGCGAGAAAACCGACCCGGAAACGGATATTGTAGTGGTGGTAGCTGCTACTCGCGGTACCCTCTACACTTGGTTCGACCCCTGG out_of_frame IGHV3-69-1*01 IGHD2-15*01 IGHJ5*02 . assemble12 0 +3 3.125000e-02 TGTGCGAGAGACCCTCCCCGGAGCAGTGGCTGGTGGGCGTCCCCTCTTCGTTTTTGACTACTGG out_of_frame IGHV3-11*01 IGHD6-19*01 IGHJ4*02 IGHM assemble5 0 +3 3.125000e-02 TGTGCGAGACAAGTGGGAGCGACCCTCATGATGCTTTTGATATCTGG out_of_frame IGHV5-51*01 IGHD1-26*01 IGHJ3*02 IGHM assemble11 0 +3 3.125000e-02 TGTGCGAAGGAGGTTGGGTGGTGACTGCTAGGGAAACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV3-NL1*01 IGHD2-21*02 IGHJ6*02 . assemble3 0 +3 3.125000e-02 TGTGCGAGCGCAGCACGGGATATTGTAGTGGTGGTAGCTGCTACGGTTCATTTATGACTACTGG out_of_frame IGHV3-11*04 IGHD2-15*01 IGHJ4*02 IGHM assemble26 0 +3 3.125000e-02 TGTGCGAAAGATCTAGGAAAGGTAGTCGCCGTATAGCAGCTCGTCCGGAGGGGATTTCTTCCTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV3-NL1*01 IGHD6-6*01 IGHJ6*02 . assemble36 0 +3 3.125000e-02 TGTGCGAGAAATGGGAGTTCGGATTTTGATCCAATCTCCTCGGGGGATTGTAGTAGTACCAGCTGCCTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-18*01 IGHD2-15*01 IGHJ6*04 IGHM assemble13 0 +3 3.125000e-02 TGTGCAAGAGATGTAGGAGGGGTATTTCCATTGTAGTGGTGGTAGCTGCTATGCTGGTTCGACCCCTGG CARDVGGVFPL_WW_LLCWFDPW IGHV3-74*01 IGHD2-15*01 IGHJ5*02 IGHM assemble25 0 +2 2.083333e-02 TGTGCGAGAGAGGGATAGCAGTGGCTTGGGTACTACTACTACTACATGGACGTCTGG CAREG_QWLGYYYYYMDVW IGHV5-51*01 IGHD6-19*01 IGHJ6*03 . assemble40 0 +2 2.083333e-02 TGTGTGTCCCTCAGAATTACTATGGTTCAGATTCGAACTCGAAGAACTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-NL1*01 IGHD3-10*01 IGHJ6*04 IGHM assemble28 0 +2 2.083333e-02 TGTGGGGTTCGGGGAGTTAACATCGATAAGAAGTAATACTACTACTACTACGGTATGGACGTCTGG CGVRGVNIDKK_YYYYYGMDVW IGHV3-49*02 IGHD3-10*01 IGHJ6*02 IGHM assemble61 0 +2 2.083333e-02 TGTGCGAGAGTGCAAGTGACCTAATAGCAGTGGCTGGTACGATTCCATACTTTGACTACTGG out_of_frame IGHV1-46*01 IGHD6-19*01 IGHJ4*02 IGHM assemble64 0 +2 2.083333e-02 TGTGCGGCTTTACTATGGTTCAGCCCGGGGTGCTTTTGATATCTGG out_of_frame IGHV3-41*02 IGHD3-10*01 IGHJ3*02 IGHM assemble33 0 +2 2.083333e-02 TGTGCGAGGGTACCCCGCGATGATAGTAGTGGTTAAACAACCCTTTGACTACTGG out_of_frame IGHV4-38-2*01 IGHD3-22*01 IGHJ4*02 IGHM assemble27 0 +2 2.083333e-02 TGTGCGAGCAACGCTGGATTGTACTGGTGGTGTATGCTAAACAATGGATTTAGATCGAGGGGAAGAAGTTACTACTACTACTACATGGACGTCTGG CASNAGLYWWCMLNNGFRSRGRSYYYYYMDVW IGHV1-69*01 IGHD2-8*02 IGHJ6*04 IGHM assemble9 0 +2 2.083333e-02 TGTGCACGGCACCCGGGTCTGTGCCTAGTATTACTATGGTTCAGGGATACTACTACTACATGGACGTCTGG out_of_frame IGHV2-70*01 IGHD3-10*01 IGHJ6*04 IGHM assemble44 0 +2 2.083333e-02 TGTGCGAAAGACGTTGCAAGCACCAGGGCACTGCCGAAACCCCCAGTTGTAGTAGTACCAGCTGCTATCCCCTTTGACTACTGG CAKDVASTRALPKPPVVVVPAAIPFDYW IGHV3-23*01 IGHD2-2*01 IGHJ4*02 IGHM assemble31 0 +2 2.083333e-02 TGTTATTGTAGTAGTACCAGCTGCTATTACTACTACTACGGTATGGACGTCTGG CYCSSTSCYYYYYGMDVW IGHV3-13*01 IGHD2-2*01 IGHJ6*02 . assemble19 0 +2 2.083333e-02 TGTAGTGGTGGTAGCTGCTATAGTAAGTACTACTTTGACGACTGG CSGGSCYSKYYFDDW IGHV3-23*01 IGHD2-15*01 IGHJ4*02 IGHM assemble46 0 +2 2.083333e-02 TGTGCAAGAGACCTAAGACATACCAGCTGCTATACTTTGACTACTGG out_of_frame IGHV3-47*01 IGHD2-2*02 IGHJ4*02 IGHM assemble15 0 +2 2.083333e-02 TGTGCGAGAGATAGGGAGTTGTAGTAGTACCAGCTGCTGTCACGGGACTACTACTACTACTACTACATGGACGTCTGG CARDREL__YQLLSRDYYYYYYMDVW IGHV3-11*04 IGHD2-2*01 IGHJ6*04 IGHM assemble30 0 +2 2.083333e-02 TGTGCGAGAGATATTGTTGTAGTGGTGGTAGCTGCTACTCCCAGGGCCCAAATTTACTGG CARDIVVVVVAATPRAQIYW IGHV3-66*01 IGHD2-15*01 IGHJ4*02 IGHM assemble34 0 +2 2.083333e-02 TGTGCGATGGGGTGGGTCGGTCCTCGGGCAGTACAACTGGTTCGACCCCTGG out_of_frame IGHV1-3*01 IGHD1-1*01 IGHJ5*02 . assemble39 0 +2 2.083333e-02 TGTGCGAGAGGCGATACCCGGTATTACGATTTTTGGAGTGGTTATTATCCGCAAAGAGGACCAGGGCAGTCCTACTACTACTACGGTATGGACGTCTGG CARGDTRYYDFWSGYYPQRGPGQSYYYYGMDVW IGHV3-11*04 IGHD3-3*01 IGHJ6*02 IGHM assemble41 0 +1 1.041667e-02 TGTGTGAGAGGGGCCATCCCCTACGGTGAGTAAACACGAATATTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV3-52*01 IGHD4-23*01 IGHJ6*04 IGHM assemble60 0 +1 1.041667e-02 TGTGCGAGAGACCCCTATTACTATGATAGTAGTGGTTATATGCCGTGACCCAGCTCGACCCCTGG out_of_frame IGHV4-61*01 IGHD3-22*01 IGHJ5*02 . assemble79 0 +1 1.041667e-02 TGTGCGAGGACCGGCCCTATAGCAGTGGCTGGTTTCACTAGGTTACTGG out_of_frame IGHV1-46*01 IGHD6-19*01 IGHJ4*02 . assemble77 0 +1 1.041667e-02 TGTGCGAGAGATGAGATTACGATATTTTGACTGGTTATTATCTGACCGAGCTGGTTTTGAGTTCCCTGAAATCCACCTAACCTGCGCAACTACTGG CARDEITIF_LVII_PSWF_VP_NPPNLRNYW IGHV1-3*01 IGHD3-9*01 IGHJ4*02 . assemble57 0 +1 1.041667e-02 TGTGCGAACGGAGGCAGCAGAAAGGTGTCTTGGGATGGTTCGACCCCTGG out_of_frame IGHV3-NL1*01 IGHD3-10*01 IGHJ5*02 . assemble53 0 +1 1.041667e-02 TGTGCGAGAGACTTAGCAGTGGCTCCCCCGGCTAGTACTACTTTGACTACTGG out_of_frame IGHV1-2*04 IGHD4-17*01 IGHJ4*02 IGHM assemble7 0 +1 1.041667e-02 TGTGCGAGAGATGGAAGCGGCGTATTACGATTTTTGGAGTGGTTCTTCCGACCATACTACTACTACTACATGGACGTCTGG CARDGSGVLRFLEWFFRPYYYYYMDVW IGHV3-11*04 IGHD3-3*01 IGHJ6*04 IGHM assemble67 0 +1 1.041667e-02 TGTGCGAGAGACCTCGGCCGTAGGTATAGCAGTGGCTGGTTCTGTTTCGACCCCTGG CARDLGRRYSSGWFCFDPW IGHV3-71*01 IGHD6-19*01 IGHJ5*02 . assemble17 0 +1 1.041667e-02 TGTGCGAAAGATATACTAGTATGATAGTAGTGGTTATGGGTTCATTGTTTACTACTGG out_of_frame IGHV3-NL1*01 IGHD3-22*01 IGHJ4*02 IGHM assemble75 0 +1 1.041667e-02 TGTGCGAGAGCTGTAACTTATATTGTAGTAGTACCAGCTGCGGGCTGACAGTTTACTACTACTACTACGGTATGGACGTCTGG out_of_frame IGHV1-3*01 IGHD2-2*01 IGHJ6*02 IGHM assemble50 0 +1 1.041667e-02 TGTGCGAAAGATAGTAGTGGCTACGATTGAATGTTGACTACTGG out_of_frame IGHV3-NL1*01 IGHD5-12*01 IGHJ4*02 . assemble58 0 +1 1.041667e-02 TGTGCGAGAGACCGGCGTTCGTGATACAGCTATGGTTACCGGACACTCCTACTACTACATGGACGTCTGG out_of_frame IGHV1-18*01 IGHD5-18*01 IGHJ6*04 IGHM assemble49 0 +1 1.041667e-02 TGTGCGAGAGATCGGAGATACCCCTTGACAAGGTATAGCAGTGGCTGGTACGAAATTAATGATGCTTTTGATATCTGG CARDRRYPLTRYSSGWYEINDAFDIW IGHV3-11*01 IGHD6-19*01 IGHJ3*02 . assemble69 0 +1 1.041667e-02 TGTGCGAAAGATCTCCCGAACTTATGTATATGTCTGGTGGTTCGACCCCTGG out_of_frame IGHV3-NL1*01 IGHD2-8*02 IGHJ5*02 IGHM assemble56 0 diff --git a/main.cpp b/main.cpp index 3c6e647..6ac9aab 100644 --- a/main.cpp +++ b/main.cpp @@ -25,6 +25,7 @@ char usage[] = "./trust4 [OPTIONS]:\n" "\t-o STRING: prefix of the output file (default: trust)\n" "\t-t INT: number of threads (default: 1)\n" "\t-c STRING: the path to the kmer count file\n" + "\t-k INT: the starting k-mer size for indexing contigs (default: 9)\n" "\t--skipMateExtension: skip the step of extension assemblies with mate-pair information\n" ///"\t--noV: do not assemble the full length V gene (default: not used)\n" "\t--trimLevel INT: 0: no trim; 1: trim low quality; 2: trim unmatched (default: 1)\n" @@ -41,7 +42,7 @@ char numToNuc[26] = {'A', 'C', 'G', 'T'} ; char buffer[10240] = "" ; -static const char *short_options = "f:u:1:2:b:o:c:t:" ; +static const char *short_options = "f:u:1:2:b:o:c:t:k:" ; static struct option long_options[] = { { "debug-ns", required_argument, 0, 10000 }, { "trimLevel", required_argument, 0, 10001 }, @@ -274,6 +275,11 @@ int main( int argc, char *argv[] ) { threadCnt = atoi( optarg ) ; } + else if ( c == 'k' ) + { + indexKmerLength = atoi( optarg ) ; + seqSet.ChangeKmerLength( indexKmerLength ) ; + } else if ( c == 10000 ) //debug-ns { seqSet.InputNovelFa( optarg ) ; diff --git a/run-trust4 b/run-trust4 index 43ed298..fd108ed 100755 --- a/run-trust4 +++ b/run-trust4 @@ -7,7 +7,7 @@ use Cwd 'cwd' ; use Cwd 'abs_path' ; use File::Basename ; -die "TRUST4 v1.0.8-r419 usage: ./run-trust4 [OPTIONS]:\n". +die "TRUST4 v1.0.8-r424 usage: ./run-trust4 [OPTIONS]:\n". "Required:\n". #"\t[Input]:\n". "\t-b STRING: path to bam file\n". @@ -19,6 +19,7 @@ die "TRUST4 v1.0.8-r419 usage: ./run-trust4 [OPTIONS]:\n". "\t-o STRING: prefix of output files. (default: inferred from file prefix)\n". "\t--od STRING: the directory for output files. (default: ./)\n". "\t-t INT: number of threads (default: 1)\n". + "\t-k INT: the starting k-mer size for indexing contigs (default: 9)\n". #"\t-h: print help message and exit.\n" "\t--barcode STRING: if -b, bam field for barcode; if -1 -2/-u, file containing barcodes (default: not used)\n". "\t--barcodeRange INT INT CHAR: start, end(-1 for length-1), strand in a barcode is the true barcode (default: 0 -1 +)\n". @@ -150,6 +151,11 @@ for ( $i = 0 ; $i < @ARGV ; ++$i ) $mainArgs .= " ".$ARGV[$i]." ".$ARGV[$i + 1] ; ++$i ; } + elsif ( $ARGV[$i] eq "-k" ) + { + $mainArgs .= " ".$ARGV[$i]." ".$ARGV[$i + 1] ; + ++$i ; + } elsif ( $ARGV[$i] eq "--abnormalUnmapFlag" ) { $bamExtractorArgs .= " -u" ;