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Version changelog

  • 2.2.0:
    • Add --no-clip to assign a barcode pair, but not clip barcode sequences from reads
    • Output .consensusreadset.xml for CCS/HiFi input
    • Add --biosample-csv to assign bio sample names to barcode pairs
    • Better help description for --peek-guess in combination with --ccs and --isoseq
    • Optional performance improvements
  • 2.1.0:
    • SMRT Link v10.1 release
    • Do not allow double hyphen in barcode name
  • 2.0.1:
    • SMRT Link v10.0 release
    • Minor fixes
  • 2.0.0:
    • Add support for FASTA and FASTQ
    • Fix -k with by-strand HiFi reads
  • 1.11.0:
    • Add barcode to read groups, use one barcode pair per RG
    • Fix double demux, used to clip wrongly for the second round of demuxing
  • 1.10.0:
    • Output N barcodes per subdirectory with --files-per-directory N and output splitting
    • BioSample awareness for XML input and split output and allow ignoring them with --ignore-biosamples
    • Increase --window-size-mult to 3 to allow longer spacers
    • Do not report no adapter hits as too short inserts
    • Increase --guess barcode score to 75 if --peek-guess --ccs are combined
    • Enable double demux of CCS data
    • Print run time, CPU time, and peak memory consumption with --log-level INFO
    • New CLI UX
  • 1.9.0:
    • Add --bad-adapter-ratio to remove ZMWs with molecularly missing adapters
    • Fix rare case, where a read only matches one barcode and not a single alternative
    • Fix --no-bam to automatically omit pbi
    • Allow combination of --isoseq with --peek-guess
  • 1.8.0:
    • Add clip lengths as bx tag
    • Enable single-barcode samples
    • Implicitly call --dump-clips in --isoseq mode
  • 1.7.1: Fix rare-care PBI generation bug, included in SMRT Link 6.0.0

  • 1.7.0: Fix corner-case bug

  • 1.6.1: Fix --min-end-score in combination with --isoseq

  • 1.6.0:
    • New filter --min-end-score
    • Add latest filters to summary file
    • New IsoSeq default parameters
    • Fix streaming of asymmetric BAM files
  • 1.5.0: Support spacer sequence between adapter and barcode

  • 1.4.0:
    • New filter --min-ref-span and --min-scoring-regions
    • Single-side library improvements
  • 1.3.0: --peek-guess uses only full-length ZMWs

  • 1.2.0:
    • Streaming of split BAM files
    • New fat binary build approach
  • 1.1.0: IsoSeq support

  • 1.0.0: Initial release, included in SMRT Link 5.1.0

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