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ReadQC tool help

ReadQC (2023_03-63-gec44de43)

Calculates QC metrics on unprocessed NGS reads.

Mandatory parameters:
  -in1 <filelist>          Forward input gzipped FASTQ file(s).

Optional parameters:
  -in2 <filelist>          Reverse input gzipped FASTQ file(s) for paired-end mode (same number of cycles/reads as 'in1').
                           Default value: ''
  -out <file>              Output qcML file. If unset, writes to STDOUT.
                           Default value: ''
  -txt                     Writes TXT format instead of qcML.
                           Default value: 'false'
  -out1 <file>             If set, writes merged forward FASTQs to this file (gzipped).
                           Default value: ''
  -out2 <file>             If set, writes merged reverse FASTQs to this file (gzipped)
                           Default value: ''
  -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'.

ReadQC changelog

ReadQC 2023_03-63-gec44de43

2023-04-18 Added support for LongRead
2021-02-03 Added option to write out merged input FASTQs (out1/out2).
2016-08-19 Added support for multiple input files.

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