kmer-mask - mask and filter set of nucleotide sequences by kmer
content
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
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.
- -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.
- -o out
- -m min-size
- ignore database hits below this many consecutive kmers (0)
- -e extend-size
- extend database hits across this many missing kmers (0)
- -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