quorum_error_correct_reads - error correct reads from a fastq file
based on the k-mer frequencies
error_correct_reads [options] db:path
sequence:path+
Error correct reads from a fastq file based on the k-mer
frequencies.
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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.