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| # SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | ||
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| - **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit) | ||
| ([**Usage**](http://bioinf.shenwei.me/seqkit/usage/), | ||
| [**FAQ**](http://bioinf.shenwei.me/seqkit/faq/), | ||
| [**Tutorial**](http://bioinf.shenwei.me/seqkit/tutorial/), | ||
| and | ||
| [**Benchmark**](http://bioinf.shenwei.me/seqkit/benchmark/)) | ||
| - **Source code:** [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit) | ||
| [](https://github.com/shenwei356/seqkit) | ||
| [](https://github.com/shenwei356/seqkit/blob/master/LICENSE) | ||
| - **Latest version:** [](https://github.com/shenwei356/seqkit/releases) | ||
| [](http://bioinf.shenwei.me/seqkit/download/) | ||
| [](http://bioinf.shenwei.me/seqkit/download/) | ||
| [](https://anaconda.org/bioconda/seqkit) | ||
| - **[Please cite](#citation):** [](https://doi.org/10.1371/journal.pone.0163962) | ||
| [](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:zYLM7Y9cAGgC) | ||
| - **Others**: [](https://biotreasury.rjmart.cn/#/tool?id=10081) | ||
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| ## Features | ||
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| - **Easy to install** ([download](http://bioinf.shenwei.me/seqkit/download/)) | ||
| - Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) | ||
| - Light weight and out-of-the-box, no dependencies, no compilation, no configuration | ||
| - `conda install -c bioconda seqkit` | ||
| - **Easy to use** | ||
| - Ultrafast (see [technical-details](http://bioinf.shenwei.me/seqkit/usage/#technical-details-and-guides-for-use) and [benchmark](http://bioinf.shenwei.me/seqkit/benchmark)) | ||
| - Seamlessly parsing both FASTA and FASTQ formats | ||
| - Supporting (`gzip`/`xz`/`zstd`/`bzip2` compressed) STDIN/STDOUT and input/output file, easily integrated in pipe | ||
| - Reproducible results (configurable rand seed in `sample` and `shuffle`) | ||
| - Supporting custom sequence ID via regular expression | ||
| - Supporting [Bash/Zsh autocompletion](http://bioinf.shenwei.me/seqkit/download/#shell-completion) | ||
| - **Versatile commands** ([usages and examples](http://bioinf.shenwei.me/seqkit/usage/)) | ||
| - Practical functions supported by [38 subcommands](#subcommands) | ||
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| ## Installation | ||
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| Go to [Download Page](http://bioinf.shenwei.me/seqkit/download) for more download options and changelogs, or | ||
| install via conda: | ||
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| conda install -c bioconda seqkit | ||
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| ## Subcommands | ||
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| |Category |Command |Function |Input |Strand-sensitivity|Multi-threads| | ||
| |:----------------|:-------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------|:-----------------|:------------| | ||
| |Basic operation |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |Transform sequences: extract ID/seq, filter by length/quality, remove gaps… |FASTA/Q | | | | ||
| | |[stats](https://bioinf.shenwei.me/seqkit/usage/#stats) |Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… |FASTA/Q | |✓ | | ||
| | |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |Get subsequences by region/gtf/bed, including flanking sequences |FASTA/Q |+ or/and - | | | ||
| | |[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding) |Extract subsequences in sliding windows |FASTA/Q |+ only | | | ||
| | |[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx) |Create the FASTA index file and extract subsequences (with more features than samtools faidx)|FASTA |+ or/and - | | | ||
| | |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | | | ||
| | |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |Monitoring and online histograms of sequence features |FASTA/Q | | | | ||
| | |[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ) |Real time concatenation and streaming of fastx files |FASTA/Q | |✓ | | ||
| |Format conversion|[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa) |Convert FASTQ to FASTA format |FASTQ | | | | ||
| | |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab) |Convert FASTA/Q to tabular format |FASTA/Q | | | | ||
| | |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |Retrieve corresponding FASTQ records by a FASTA file |FASTA/Q |+ only | | | ||
| | |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |TSV | | | | ||
| | |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |Convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | | | ||
| |Searching |[grep](https://bioinf.shenwei.me/seqkit/usage/#grep) |Search sequences by ID/name/sequence/sequence motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m | | ||
| | |[locate](https://bioinf.shenwei.me/seqkit/usage/#locate) |Locate subsequences/motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m | | ||
| | |[amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon) |Extract amplicon (or specific region around it), mismatch allowed |FASTA/Q |+ and - |partly, -m | | ||
| | |[fish](https://bioinf.shenwei.me/seqkit/usage/#fish) |Look for short sequences in larger sequences |FASTA/Q |+ and - | | | ||
| |Set operation |[sample](https://bioinf.shenwei.me/seqkit/usage/#sample) |Sample sequences by number or proportion |FASTA/Q | | | | ||
| | |[rmdup](https://bioinf.shenwei.me/seqkit/usage/#rmdup) |Remove duplicated sequences by ID/name/sequence |FASTA/Q |+ and - | | | ||
| | |[common](https://bioinf.shenwei.me/seqkit/usage/#common) |Find common sequences of multiple files by id/name/sequence |FASTA/Q |+ and - | | | ||
| | |[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate) |Duplicate sequences N times |FASTA/Q | | | | ||
| | |[split](https://bioinf.shenwei.me/seqkit/usage/#split) |Split sequences into files by id/seq region/size/parts (mainly for FASTA) |FASTA preffered| | | | ||
| | |[split2](https://bioinf.shenwei.me/seqkit/usage/#split2) |Split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | | | ||
| | |[head](https://bioinf.shenwei.me/seqkit/usage/#head) |Print first N FASTA/Q records |FASTA/Q | | | | ||
| | |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |Print sequences of the first genome with common prefixes in name |FASTA/Q | | | | ||
| | |[range](https://bioinf.shenwei.me/seqkit/usage/#range) |Print FASTA/Q records in a range (start:end) |FASTA/Q | | | | ||
| | |[pair](https://bioinf.shenwei.me/seqkit/usage/#pair) |Patch up paired-end reads from two fastq files |FASTA/Q | | | | ||
| |Edit |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |Replace name/sequence by regular expression |FASTA/Q |+ only | | | ||
| | |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |Rename duplicated IDs |FASTA/Q | | | | ||
| | |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |Concatenate sequences with same ID from multiple files |FASTA/Q |+ only | | | ||
| | |[restart](https://bioinf.shenwei.me/seqkit/usage/#restart) |Reset start position for circular genome |FASTA/Q |+ only | | | ||
| | |[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate) |Edit sequence (point mutation, insertion, deletion) |FASTA/Q |+ only | | | ||
| | |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |Sanitize broken single line FASTQ files |FASTQ | | | | ||
| |Ordering |[sort](https://bioinf.shenwei.me/seqkit/usage/#sort) |Sort sequences by id/name/sequence/length |FASTA preffered| | | | ||
| | |[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle) |Shuffle sequences |FASTA preffered| | | | ||
| |BAM processing |[bam](https://bioinf.shenwei.me/seqkit/usage/#bam) |Monitoring and online histograms of BAM record features |BAM | | | | ||
| |Miscellaneous |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |Compute message digest for all sequences in FASTA/Q files |FASTA/Q | |✓ | | ||
| | |[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides)|Merge sliding windows generated from seqkit sliding |TSV | | | ||
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| Notes: | ||
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| - Strand-sensitivity: | ||
| - `+ only`: only processing on the positive/forward strand. | ||
| - `+ and -`: searching on both strands. | ||
| - `+ or/and -`: depends on users' flags/options/arguments. | ||
| - Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads. | ||
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| ## Citation | ||
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| **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. | ||
| ***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962). | ||
| <span class="__dimensions_badge_embed__" data-doi="10.1371/journal.pone.0163962" data-style="small_rectangle"></span> | ||
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| ## Contributors | ||
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| - [Wei Shen](https://github.com/shenwei356) | ||
| - [Botond Sipos](https://github.com/botond-sipos): `bam`, `scat`, `fish`, `sana`, `watch`. | ||
| - [others](https://github.com/shenwei356/seqkit/graphs/contributors) | ||
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| ## Acknowledgements | ||
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| We thank [Lei Zhang](https://github.com/jameslz) for testing SeqKit, | ||
| and also thank [Jim Hester](https://github.com/jimhester/), | ||
| author of [fasta_utilities](https://github.com/jimhester/fasta_utilities), | ||
| for advice on early performance improvements of for FASTA parsing | ||
| and [Brian Bushnell](https://twitter.com/BBToolsBio), | ||
| author of [BBMaps](https://sourceforge.net/projects/bbmap/), | ||
| for advice on naming SeqKit and adding accuracy evaluation in benchmarks. | ||
| We also thank Nicholas C. Wu from the Scripps Research Institute, | ||
| USA for commenting on the manuscript | ||
| and [Guangchuang Yu](http://guangchuangyu.github.io/) | ||
| from State Key Laboratory of Emerging Infectious Diseases, | ||
| The University of Hong Kong, HK for advice on the manuscript. | ||
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| We thank [Li Peng](https://github.com/penglbio) for reporting many bugs. | ||
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| We appreciate [Klaus Post](https://github.com/klauspost) for his fantastic packages ( | ||
| [compress](https://github.com/klauspost/compress) and [pgzip](https://github.com/klauspost/pgzip) | ||
| ) which accelerate gzip file reading and writing. | ||
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| ## Contact | ||
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| [Create an issue](https://github.com/shenwei356/seqkit/issues) to report bugs, | ||
| propose new functions or ask for help. | ||
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| ## License | ||
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| [MIT License](https://github.com/shenwei356/seqkit/blob/master/LICENSE) | ||
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| ## Starchart | ||
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| <img src="https://starchart.cc/shenwei356/seqkit.svg" alt="Stargazers over time" style="max-width: 100%"> | ||
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