NAME

       quorum - run quorum error corrector on fastq file

DESCRIPTION

       quorum [options] <fastq> [fastq]

DESCRIPTION

       Run  the  quorum  error corrector on the given fastq file. If the --paired-files switch is
       given, quorum expect an even number  of  files  on  the  command  line,  each  pair  files
       containing  pair end reads. The output will be two files (<prefix>_1.fa and <prefix>_2.fa)
       containing error corrected pair end reads.

OPTIONS

       -s, --size
              Mer database size (default 200M)

       -t, --threads
              Number of threads (default number of cpus)

       -p, --prefix
              Output prefix (default quorum_corrected)

       -k, --kmer-len
              Kmer length (default 24)

       -q, --min-q-char
              Minimum quality char. Usually 33 or 64 (autodetect)

       -m, --min-quality
              Minimum above -q for high quality base (5)

       -w, --window
              Window size for trimming

       -e, --error
              Maximum number of errors in a window

       --min-count
              Minimum count for a k-mer to be good

       --skip Number of bases to skip to find anchor kmer

       --anchor
              Numer of good kmer in a row for anchor

       --anchor-count
              Minimum count for an anchor kmer

       --contaminant
              Contaminant sequences

       --trim-contaminant
              Trim sequences with contaminant mers

       -d, --no-discard
              Do not discard reads, output a single N (false)

       -P, --paired-files
              Preserve mate pairs in two files

       --homo-trim
              Trim homo-polymer on 3' end

       --debug
              Display debugging information

       --version
              Display version

       -h, --help
              This message

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.