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Version changelog

  • 3.4.0
    • SMRT Link release 10.0.0
    • Add support for UMI and cell barcode handling, by adding tag and dedup
    • Add refine --min-rq to support RQ filtering for unfiltered <movie>.reads.bam input
  • 3.3.0
    • SMRT Link release 9.0.0
  • 3.2.2
    • Fix polish not generating fasta/q output. This bug was introduced in v3.2.0
  • 3.2.1
    • Fix a gff index 1-off bug in collapse
    • We have removed implicit dependencies from the bioconda recipe. Please install pbccs, lima, and pbcoretools as needed.
  • 3.2.0
    • polish dropped support for RS II datasets!
    • Add collapse step for aligned transcript BAM input
    • Enable CCS-only workflow cluster --use-qvs
    • Add refine --min-polya-length
    • Add cluster --singletons to output unclustered FLNCs; potential sample prep artifacts!
    • Fix minimap2 bugs. Outputs might change slightly.
  • 3.1.2
    • Reduce polish memory footprint
  • 3.1.1
    • Edge case fix where polish would not finish and stale
    • Improve polish run time for large scale datasets (> 1M CCS)
    • Improve polish result quality
  • 3.1.0
    • We outsourced the poly(A) tail removal and concatemer detection into a new tool called refine. Your custom primers.fasta is used in this step to detect concatemers.

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