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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
prefix for output reads

reads with below 'lowthreshold' bases retained

reads in between

reads with more than 'hightreshold' bases retained

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)

-novel RETAIN novel sequence not present in the database

RETAIN confirmed sequence present in the database

promote the lesser RETAINED read to the status of the more RETAINED read
read1=fullymasked and read2=partiallymasked -> both are partiallymasked

demote the more RETAINED read to the status of the lesser RETAINED read
read1=fullymasked and read2=partiallymasked -> both are fullymasked

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

-highthreshold t

-h histogram
write a histogram of the amount of sequence RETAINED

-t t use t compute threads

-v show progress

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