NAME
kmer-mask - mask and filter set of nucleotide sequences by kmer content
SYNOPSIS
kmer-mask {-novel|-confirmed} [-mdb mer-database] [-ms mer-size] [-edb exist-database] [-m min-size] [-e extend-size] [-lowthreshold l] [-highthreshold h] [-t threads] [-v] [-h histogram] [-promote|-demote|-discard] -1 in.1.fastq [-2 in.2.fastq] -o output-prefix
DESCRIPTION
Mask and filter set of sequences (presumed to be reads) by kmer content. Masking can be done to retain novel sequence not in the database, or to retain confirmed sequence present in the database. Filtering will segregate sequences fully, partially or not masked.
OPTIONS
-mdb mer-database
load masking kmers from meryl(1) mer-database
-ms mer-size
-edb exist-database
save masking kmers to an existDB(1) file exist-database for faster restarts
-1 in.1.fastq
-2 in.2.fastq
input reads files in fastq, fastq.gz, fastq.bz2 or fastq.xz format. The second is optional, but messes up the output classification if not present.
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-o out |
prefix for output reads |
out.fullymasked.[12].fastq
reads with below ’lowthreshold’ bases retained
out.partiallymasked.[12].fastq
reads in between
out.retained.[12].fastq
reads with more than ’hightreshold’ bases retained
out.discarded.[12].fastq
reads with conflicting status
-m min-size
ignore database hits below this many consecutive kmers (0)
-e extend-size
extend database hits across this many missing kmers (0)
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-novel |
RETAIN novel sequence not present in the database |
-confirmed
RETAIN confirmed sequence present in the database
-promote
promote the lesser RETAINED read to the status of the more RETAINED read read1=fullymasked and read2=partiallymasked -> both are partiallymasked
-demote
demote the more RETAINED read to the status of the lesser RETAINED read read1=fullymasked and read2=partiallymasked -> both are fullymasked
-discard
discard pairs with conflicting status (DEFAULT) read1=fullymasked and read2=partiallymasked -> both are discarded
stats on
stderr, number of sequences with amount RETAINED:
-lowthreshold t
(0.3333)
-highthreshold t
(0.6667)
-h histogram
write a histogram of the amount of sequence RETAINED
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-t t |
use t compute threads |
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-v |
show progress |