4.2.0 SMRT Link v25.1 release Update PM to show platform name Update RGID to match molecule read name for groupdedup / dedup 4.1.0 Update minimap2 to version 2.26 SMRT Link v13.0 release 4.0.0 Rename isoseq3 to isoseq Add new tool isoseq cluster2 Update --max-5p-diff default value for isoseq collapse Add X design option to isoseq tag to remove TSO sequences 3.8.2 Update groupdedup to output consistent molecular IDs across runs Bug fix updating rc and gp tags to passing for subset of correct reads 3.8.1 Real-cell --method and --percentile options added to correct 3.8.0 collapse allows isoforms with 5p degradation to collapse by default--do-not-collapse-extra-5exons added to collapsecollapse max 5p and 3p distances can be set in CLI using --max-5p-diff and --max-3p-diffReal-cell annotation in correct using rc tag Real-cell filtering in groupdedup, dedup, and collapse 3.7.0 Adding bcstats, correct, and groupdedup to CLI bcstats emits frequency statistics for 10x barcodescorrect uses a truth-set to correct sequencing errors in cell barcodesgroupdedup provides substantial performance improvements over dedupSupport SEGMENT read type 3.6.0 Adding tag and dedup to CLI 3.5.0 SMRT Link release 11.0 Remove support for CLR data and disable polish step Enable cluster --use-qvs as always on 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 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 THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.