Changelog (original) (raw)

Version changelog

8.0.1

• SMRT Link v13.1 release
• No customer-facing changes

8.0.0

• SMRT Link v13.0 release
• Always encode HiFi kinetics with v1 codec
• Add fail flag ff

7.0.0

• SMRT Link v12.0 release
• Includes DeepConsensus polishing on the Revio platform
• Arrow polishing on GPU on the Revio platform
• New output files layout
• Output BAM file compression

6.4.0

• Single-strand HiFi kinetics
• Faster draft generation
• CLR subsampling stores XML and PBI

6.3.0

• SMRT Link v11.0 release
• Heteroduplex finder
  • Change file output, single file with multiple read groups
  • Add HD detection for substitutions differences between strands
• Add missing adapter tags ma and ac
• Adhere to latest PacBio BAM spec
• Add --subsample-clr-perc and --subsample-clr-file to store a percentage of productive ZMWs as subreads
• Add --fastq as an additional output file

6.2.0

• SMRT Link v10.2 release
• Improved low-complexity handling, better runtime and lower memory usage
• Improved BAM merge step, up to 5x faster
• Improved compute run time
• INFO logging if chemistry bundle is injected
• Enable strand splitting of ZMWs that contain large insertion heteroduplexes
• Use TMPDIR environment variable for storing temporary files
• New INFO log summary and ccs_reports.txt

6.0.0

• SMRT Link v10.1 release
• 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