NAME

       bloomfilter.sh - Filters reads potentially sharing a kmer with a reference

SYNOPSIS

       bloomfilter.sh in=<input file> out=<nonmatches> outm=<matches> ref=<reference>

DESCRIPTION

       Filters  reads  potentially  sharing a kmer with a reference.  The more memory, the higher
       the accuracy.  Reads going to outu are guaranteed to not match the  reference,  but  reads
       going to outm might may or may not match the reference.

EXAMPLES

       bloomfilter.sh in=reads.fq outm=nonhuman.fq outm=human.fq k=31 minhits=3 ref=human.fa

       Error correction and depth filtering can be done simultaneously.

OPTIONS

   File parameters:
       in=<file>
              Primary input, or read 1 input.

       in2=<file>
              Read 2 input if reads are in two files.

       outm=<file>
              (out) Primary matched read output.

       outm2=<file>
              (out2) Matched read 2 output if reads are in two files.

       outu=<file>
              Primary unmatched read output.

       outu2=<file>
              Unmatched read 2 output if reads are in two files.

       ref=<file>
              Reference sequence file, or a comma-delimited list.

              For depth-based filtering, set this to the same as the input.

       overwrite=t
              (ow)  Set  to false to force the program to abort rather than overwrite an existing
              file.

   Hashing parameters:
       k=31   Kmer length.

       hashes=2
              Number of hashes per kmer.  Higher generally reduces false positives at the expense
              of speed.

       minprob=0.5
              Ignore  reference kmers with probability of being correct below this (affects fastq
              references only).

       memmult=1.0
              Fraction of free memory to use for Bloom filter.  1.0 should generally work; if the
              program  crashes  with  an  out  of memory error, set this lower.  Higher increases
              specificity.

       cells= Option to set the number of cells manually.  By default this will be autoset to use
              all  available  memory.   The  only  reason  to set this is to ensure deterministic
              output.

       seed=0 This will change the hash function used.

   Reference-matching parameters:
       minhits=3
              Consecutive kmer hits for a read to be considered matched.

              Higher reduces false positives at the expense of sensitivity.

       mincount=1
              Minimum number of times a read kmer must occur in the reference to be considered  a
              match.

       requireboth=f
              Require both reads in a pair to match the ref in order to go to outm.

              By default, pairs go to outm if either matches.

   Java Parameters
       -Xmx   This will set Java's memory usage, overriding autodetection.

              -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. The max is
              typically 85% of physical memory.

       -eoom  This flag will cause the process to exit  if  an  out-of-memory  exception  occurs.
              Requires Java 8u92+.

       -da    Disable assertions.

AUTHOR

       Written by Brian Bushnell

       Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.