New features Adds '--umi-separator' option to umi_tools extract to specify UMI separator. Thanks @opplatek (#548) Optimisation Speeds up read pair mate writing. Significant benefit for transcriptome alignments (#543) Bugfix Handles umi_tools group output to tsv with --per-contig when no gene tags are present. Thanks @mfansler & @akmorrow13 (#577) Fixes syntax warning in extract.py. Thanks @rajivnarayan (#558) Improves error message for incorrect command line input. Thanks @epruesse (#506 & #537
Improves the group command: Adds the --subset option as per the dedup command (#74) Corrects the fl...
When investigating differences in expression matrixes generated by 10x and our software, we discover...
Bugfix whitelist --filtered-out with SE reads threw an unassigned error. Thanks @yech1990 for recti...
New features Adds '--umi-separator' option to umi_tools extract to specify UMI separator. Thanks @o...
Added functionality: Deduplicating on gene ids ( #44 for motivation): The user can now group/dedup ...
Added functionality: Deduplicating on gene ids ( #44 for motivation): The user can now group/dedup ...
Adds the new group command to group PCR duplicates and return the groups in a tagged BAM file and/or...
Tweaks the way group handles paired end BAMs. To simplify the process and ensure all reads are writt...
A long overdue release covering some minor functionality updates and bugfixes: Additional functional...
Version 0.5.0 introduces new commands to support single-cell RNA-Seq and reduces run-time. The under...
Minor update. Improves detection of duplicate reads with paired end reads, reduces run time with ded...
Adds options to specify a delimiter for a cell barcode or UMI which should be concatenated + options...
When using the directional method with the group command, the 'top' UMI within each group was not al...
When using the directional method with the group command, the 'top' UMI within each group was not al...
Adds options to specify a delimiter for a cell barcode or UMI which should be concatenated + option...
Improves the group command: Adds the --subset option as per the dedup command (#74) Corrects the fl...
When investigating differences in expression matrixes generated by 10x and our software, we discover...
Bugfix whitelist --filtered-out with SE reads threw an unassigned error. Thanks @yech1990 for recti...
New features Adds '--umi-separator' option to umi_tools extract to specify UMI separator. Thanks @o...
Added functionality: Deduplicating on gene ids ( #44 for motivation): The user can now group/dedup ...
Added functionality: Deduplicating on gene ids ( #44 for motivation): The user can now group/dedup ...
Adds the new group command to group PCR duplicates and return the groups in a tagged BAM file and/or...
Tweaks the way group handles paired end BAMs. To simplify the process and ensure all reads are writt...
A long overdue release covering some minor functionality updates and bugfixes: Additional functional...
Version 0.5.0 introduces new commands to support single-cell RNA-Seq and reduces run-time. The under...
Minor update. Improves detection of duplicate reads with paired end reads, reduces run time with ded...
Adds options to specify a delimiter for a cell barcode or UMI which should be concatenated + options...
When using the directional method with the group command, the 'top' UMI within each group was not al...
When using the directional method with the group command, the 'top' UMI within each group was not al...
Adds options to specify a delimiter for a cell barcode or UMI which should be concatenated + option...
Improves the group command: Adds the --subset option as per the dedup command (#74) Corrects the fl...
When investigating differences in expression matrixes generated by 10x and our software, we discover...
Bugfix whitelist --filtered-out with SE reads threw an unassigned error. Thanks @yech1990 for recti...