Man page - quorum(1)

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QUORUM

NAME
DESCRIPTION
DESCRIPTION
OPTIONS
AUTHOR

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.