Version changelog

• 2.12.0:
  • SMRT Link v25.1 release
  • Enable fail_reads input options
  • Extended clipping support for MM and ML tags
• 2.9.0:
  • SMRT Link v13.0 release
  • Add --overwrite-biosample-name option for double demux
  • Add sa, sm, and sx tags
  • Fixes for --single-end
• 2.7.1:
  • SMRT Link v12.0 release
  • Allow --single-end to only score to score only one flank
• 2.6.0:
  • Support SEGMENT read type
  • Use final MM/ML basemod tags
  • Bug fixes
• 2.5.0:
  • Upcoming SMRT Link release
  • Add lima-undo functionality
  • Support methylation tag clipping
  • Add progress and ETA for --log-level INFO
  • Rename --preset to --hifi-preset
  • Add barcoded adapter --hifi-preset SYMMETRIC-ADAPTERS
  • Fixes to support stranded HiFi BAM input
  • Do not abort on empty input, but warn only
• 2.4.0:
  • Fix fasta/q input and --guess
  • Output empty files for missing barcode pairs --output-missing-pairs
  • Output each barcode into its own sub-directory --split-subdirs
  • Passthrough of input ExternalResources in XML
  • Add Provenance element to XML output
  • Do not override Sample tag SM in read group if --isoseq is used
  • Enable --reuse-uuids with --biosample-csv
  • Add --reuse-source-uuid from input XML
  • Store BioSamples under WellSample
  • Allow --dataset-name to override dataset name attribute
• 2.3.0:
  • SMRT Link v10.2 release
  • Add --preset for HIFI-SYMMETRIC and HIFI-ASYMMETRIC
• 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