quorum1

Overview

quorum [options] <fastq> [fastq]

Overview

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