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:
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-t, --thread=uint32 -
Number of threads (1)
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-m, --min-count=uint32 -
Minimum count for a k-mer to be considered "good" (1)
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-s, --skip=uint32 -
Number of bases to skip for start k-mer (1)
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-g, --good=uint32 -
Number of good k-mer in a row for anchor (2)
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-a, --anchor-count=uint32 -
Minimum count for an anchor k-mer (3)
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-w, --window=uint32 -
Size of window (10)
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-e, --error=uint32 -
Maximum number of error in a window (3)
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-o, --output=prefix -
Output file prefix (error_corrected)
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--contaminant=path -
Jellyfish database of contaminant k-mers
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--trim-contaminant -
Trim reads containing contaminated k-mers instead of discarding (false)
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--homo-trim=int32 -
Trim homo-polymer run at the 3' end
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--gzip -
Gzip output file (false)
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-M, --no-mmap -
Do not memory map the input mer database (false)
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--apriori-error-rate=double -
Probability of a base being an error (0.01)
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--poisson-threshold=double -
Error probability threshold in Poisson test (1.0e-06)
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-p, --cutoff=uint32 -
Poisson cutoff when there are multiple choices
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-q, --qual-cutoff-value=uint32 -
Any base above with quality equal or greater is untouched when there are multiple choices
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-Q, --qual-cutoff-char=string -
Any base above with quality equal or greater is untouched when there are multiple choices
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-d, --no-discard -
Do not discard reads, output a single N (false)
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-v, --verbose -
Be verbose (false)
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-U, --usage -
Usage
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-h, --help -
This message
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-V, --version -
Version