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FastqExtractUMI.md

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FastqExtractUMI tool help

FastqExtractUMI (2020_03-159-g5c8b2e82)

Cuts UMI bases from the beginning of reads and adds them to read headers.

Mandatory parameters:
  -in1 <file>              Input FASTQ file 1.
  -in2 <file>              Input FASTQ file 2.
  -out1 <file>             Output filename for read 1 FASTQ.
  -out2 <file>             Output filename for read 2 FASTQ.

Optional parameters:
  -cut1 <int>              Number of bases from the head of read 1 to use as UMI.
                           Default value: '0'
  -cut2 <int>              Number of bases from the head of read 2 to use as UMI.
                           Default value: '0'
  -compression_level <int> Output FASTQ compression level from 1 (fastest) to 9 (best compression).
                           Default value: '1'

Special parameters:
  --help                   Shows this help and exits.
  --version                Prints version and exits.
  --changelog              Prints changeloge and exits.
  --tdx                    Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

FastqExtractUMI changelog

FastqExtractUMI 2020_03-159-g5c8b2e82

2020-07-15 Added 'compression_level' parameter.

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