NAME

CLIPSeqTools::PreprocessApp::collapse_fastq - Keep a single record for identical sequences

SYNOPSIS

clipseqtools-preprocess collapse_fastq [options/parameters]

DESCRIPTION

Collapse a fastq file. Will keep only a single record for each group of identical sequences.

OPTIONS

Input.
  --fastq <Str>          FASTQ file with sequences
  --memsave <Int>        Memory saving factor. 0 is the fastest but uses the
                         most memory. 1 uses ~1/4 of memory and ~4x time.
                         Each step (2, 3, 4 etc) changes memory and time
                         by a factor of 4. If this option is used the output
                         will be grouped by first N nucleotides.
                         [Default: 0]

Output
  --o_prefix <Str>       output path prefix. Script will create and add
                         extension to path. [Default: ./]

Other options.
  -v --verbose           print progress lines and extra information.
  -h -? --usage --help   print help message