kmer-mask - mask and filter set of nucleotide sequences by kmer content

       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.

       kmer-mask - mask and filter set of nucleotide sequences by kmer content

-mdbmer-database
              load masking kmers from meryl(1) mer-database-msmer-size-edbexist-database
              save masking kmers to an existDB(1) file exist-database for faster restarts

       -1in.1.fastq-2in.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.

       -oout
              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

       -mmin-size
              ignore database hits below this many consecutive kmers (0)

       -eextend-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

   statsonstderr,numberofsequenceswithamountRETAINED:-lowthresholdt
              (0.3333)

       -highthresholdt
              (0.6667)

       -hhistogram
              write a histogram of the amount of sequence RETAINED

       -tt   use t compute threads

       -v     show progress

meryl(1) existDB(1)

kmer-mask 0~20150520+2004                           May 2015                                        KMER-MASK(1)

kmer-mask  {-novel|-confirmed} [-mdbmer-database] [-msmer-size] [-edbexist-database] [-mmin-size] [-eextend-size]   [-lowthresholdl]   [-highthresholdh]    [-tthreads]    [-v]    [-hhistogram]
       [-promote|-demote|-discard] -1in.1.fastq [-2in.2.fastq] -ooutput-prefix