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

COPYRIGHT

       The Cooperative Computing Tools are Copyright (C) 2022 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)