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| QUORUM(1) |
User Commands |
QUORUM(1) |
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.
