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