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.