NAME

       quorum_error_correct_reads  -  error  correct  reads  from a fastq file based on the k-mer
       frequencies

SYNOPSIS

       error_correct_reads [options] db:path sequence:path+

DESCRIPTION

       Error correct reads from a fastq file based on the k-mer frequencies.

OPTIONS

       default value in (), *required:

       -t, --thread=uint32
              Number of threads (1)

       -m, --min-count=uint32
              Minimum count for a k-mer to be considered "good" (1)

       -s, --skip=uint32
              Number of bases to skip for start k-mer (1)

       -g, --good=uint32
              Number of good k-mer in a row for anchor (2)

       -a, --anchor-count=uint32
              Minimum count for an anchor k-mer (3)

       -w, --window=uint32
              Size of window (10)

       -e, --error=uint32
              Maximum number of error in a window (3)

       -o, --output=prefix
              Output file prefix (error_corrected)

       --contaminant=path
              Jellyfish database of contaminant k-mers

       --trim-contaminant
              Trim reads containing contaminated k-mers instead of discarding (false)

       --homo-trim=int32
              Trim homo-polymer run at the 3' end

       --gzip Gzip output file (false)

       -M, --no-mmap
              Do not memory map the input mer database (false)

       --apriori-error-rate=double
              Probability of a base being an error (0.01)

       --poisson-threshold=double
              Error probability threshold in Poisson test (1.0e-06)

       -p, --cutoff=uint32
              Poisson cutoff when there are multiple choices

       -q, --qual-cutoff-value=uint32
              Any base above with quality equal or greater is untouched when there  are  multiple
              choices

       -Q, --qual-cutoff-char=string
              Any  base  above with quality equal or greater is untouched when there are multiple
              choices

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

       -v, --verbose
              Be verbose (false)

       -U, --usage
              Usage

       -h, --help
              This message

       -V, --version
              Version

AUTHOR

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