focal (1) sand_filter_kernel.1.gz

Provided by: coop-computing-tools_7.0.22-1ubuntu1_amd64 bug

NAME
       sand_filter_kernel - filter read sequences sequentially


SYNOPSIS
       sand_filter_kernel [options] <sequence file> [second sequence file]


DESCRIPTION
       sand_filter_kernel  filters  a list of genomic sequences, and produces a list of candidate pairs for more
       detailed alignment.  It is not normally called by the user, but is invoked by  sand_filter_master(1)  for
       each sequential step of a distributed alignment workload.

       If  one  sequence  file  is given, sand_filter_kernel will look for similarities between all sequences in
       that file.  If given two files, it will look for similarities between sequences in the first file and the
       second  file.  The output is a list of candidate pairs, listing the name of the candidate sequences and a
       starting position for alignment.


OPTIONS
        -s <size>
              Size of "rectangle" for filtering. You can determine the size dynamically by passing in  d  rather
              than a number.

        -r <file>
              A meryl file of repeat mers to be ignored.

        -k <size>
              The k-mer size to use in candidate selection (default is 22).

        -w <number>
              The minimizer window size to use in candidate selection (default is 22).

        -o <filename>
              The output file. Default is stdout.

        -d <subsystem>
              Enable debug messages for this subsystem.  Try -d all to start.

        -v    Show version string.

        -h    Show help screen.


EXIT STATUS
       On success, returns zero.  On failure, returns non-zero.


EXAMPLES
       Users  do  not  normally  invoke  sand_filter_kernel  directly.  Instead, options such as the k-mer size,
       minimizer window, and repeat file may  be  specified  by  the  same  arguments  to  sand_filter_master(1)
       instead.   For  example,  to  run a filter with a k-mer size of 20, window size of 24, and repeat file of
       mydata.repeats:

               % sand_filter_master -k 20 -w 24 -r mydata.repeats mydata.cfa mydata.cand


       The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright (C) 2005-2015 The
       University  of  Notre  Dame.  This software is distributed under the GNU General Public License.  See the
       file COPYING for details.


SEE ALSO
       •   Cooperative Computing Tools Documentation

       •   SAND User Manual

       •   sand_filter_master(1)      sand_filter_kernel(1)      sand_align_master(1)       sand_align_kernel(1)
           sand_compress_reads(1)  sand_uncompress_reads(1)  work_queue_worker(1)