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Support for SBARRO experiments
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@jamesnemesh jamesnemesh released this 04 Aug 19:46
· 245 commits to master since this release
v2.4.1
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Learn about vigilant mode.

Support for SBARRO experiments 

  • TagReadWithRabiesBarcodes - Tags an unaligned BAM with rabies virus barcode sequences and associated metrics. Barcode sequences are extracted using invariant sequences which flank the barcode regions.
  • FilterValidRabiesBarcodes - Filters rabies virus tags into pass/fail BAMs based on metrics associated with the extracted viral barcodes.
  • BipartiteRabiesVirusCollapse - Collapse rabies virus sequences in which half the barcode matches within some edit distance, within a cell.
     

Other updates

  • TrimStartingSequence update:  New algorithm with mismatch rate and sequence not require to be anchored to start of read.  Note that different sequence is recommended for 10X and Drop-seq.  Old, buggy behavior can be enabled with LEGACY=true.
  • PolyATrimmer now optionally stores length of polyA and trimmed adapter
  • ConvertTagToReadGroup improved error messages when read group missing from input data
  • FilterBamByGeneFunction - new program to filter reads to specified gene functions, in the same way DigtialGeneExpression and related programs internally filter data.
  • CensusSeq and related software can now take as input a list of BAMs.
  • Csi analysis now generates a contamination confidence interval.
  • Improvements to make GTF parsing more robust
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