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FastqExtract tool help

FastqExtract (2024_08-110-g317f43b9)

Extracts reads from a FASTQ file according to an ID list. Trims the reads if lengths are given.

Mandatory parameters:
  -in <file>               Input FASTQ file (gzipped or plain).
  -ids <file>              Input TSV file containing IDs (without the '@') in the first column and optional length in the second column.
  -out <file>              Output FASTQ file.

Optional parameters:
  -v                       Invert match: keep non-matching reads.
                           Default value: 'false'
  -compression_level <int> Output FASTQ compression level from 1 (fastest) to 9 (best compression).
                           Default value: '1'
  -long_read               Support long reads (> 1kb).
                           Default value: 'false'

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'.
  --settings [file]        Settings override file (no other settings files are used).

FastqExtract changelog

FastqExtract 2024_08-110-g317f43b9

2023-04-18 Added support for long reads.
2020-07-15 Added 'compression_level' parameter.

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