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.

quorum 1.1.1                                        May 2017                                           QUORUM(1)