UMICollapse

note

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.

https://github.com/Daniel-Liu-c0deb0t/UMICollapse

DOI: 10.7717/peerj.8275

MIT License

Sample names are extracted from log files if possible. In logs, the command line arguments are printed, which must have both the input and output file paths.

umicollapse bam -i SRR19887568.sorted.bam -o SRR19887568.umi_dedup.sorted.bam
Arguments	[bam, -i, SRR19887568.sorted.bam, -o, SRR19887568.umi_dedup.sorted.bam]

umicollapse requires both -i and -o flags as valid file paths. Process substitution is not supported currently by umicollapse, but in case it is used for the -i flag, we fallback to the log file name.

File search patterns

umicollapse:
  contents: 'UMI collapsing finished in '
  num_lines: 100