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Version changelog

6.0.0

  • Increase number of HiFi reads
  • Increase percentage of barcode yield
  • Run time, CPU time, and peak RSS improvements
  • Change main draft algorithm from pbdagcon to sparc
  • Replace minimap2 with pancake and edlib/KSW2

5.0.0

  • SMRT Link v10.0 release
  • Add --hifi-kinetics to average kinetic information for polished reads
  • Add --all-kinetics to add kinetic information for all ZMWs, except for unpolished draft consensus
  • Add --subread-fallback, combined with --all, use a subread instead of a draft as representative consensus
  • Use sDUST to identify tandem repeats
  • Output HiFi yield (>= Q20) and Unique Molecular Yield as INFO log
  • Set --top-passes 60 default
  • Abort if chemistry information is missing in BAM header
  • Add non-blocking temporary file writing
  • Add --input-buffer to smooth IO fluctations
  • Add --all to generate one representative read per ZMW
  • Reuse prefix of output file for report files to avoid unintentional clobbering
  • Add zmw_metrics.json, metrics about each ZMW; file name can be set with --metrics-json
  • Add JSON output of ccs_reports via --report-json
  • Add --suppress-reports to suppress generating default report and metric files

4.2.0

  • SMRT Link v9.0 release
  • Speed improvements
  • Minor yield improvements, by requiring a percentage of subreads mapping back to draft instead of --min-passes
  • Add effective coverage ec tag
  • Lowering --min-passes does no longer reduce yield
  • Add --batch-size to better saturate machine with high core counts
  • Simplify log output
  • Fix bug in predicted accuracy calculation
  • Improved ccs_report.txt summary

4.1.0

  • Minor speed improvements
  • Fix --by-strand logic, see more here
  • Allow vanilla .xml output without specifying dataset type
  • Compute wall start/end for each output read (future basecaller functionality)

4.0.0

  • SMRT Link v8.0 release
  • Speed improvements
  • Removed support for legacy python Genomic Consensus, please use gcpp
  • New command-line interface
  • New report file

3.4.1

  • SMRT Link v7.0 release
  • Log used chemistry model to INFO level

3.4.0

  • Fixes to unpolished mode for IsoSeq
  • Improve runtime when --minPredictedAccuracy has been increased

3.3.0

  • Add a windowing approach to reduce computational complexity from quadratic to linear
  • Improve multi-threading framework to increase throughput
  • Enhance XML output, propagate CollectionMetadata
  • Includes latest chemistry parameters

3.1.0

  • Add --maxPoaCoverage to decrease runtime for unpolished output, special parameter for IsoSeq workflow
  • Chemistry parameters for SMRT Link v6.0