Man page - quorum_error_correct_reads(1)
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Manual
QUORUM_ERROR_CORRECT_READS
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
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.