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