quorum_error_correct_reads1
Error correct reads from a fastq file based on the k-mer frequencies
Usage
error_correct_reads [options]
db:path
sequence:path+
Overview
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
Releases
Unchanged in 4 releases since Debian 10 (Buster).