NAME

       sand_align_kernel - align candidate sequences sequentially

SYNOPSIS

       sand_align_kernel [options] [input file]

DESCRIPTION

       sand_align_kernel  aligns  candidate sequences sequentially.  It is not normally called by
       the user, but is invoked by sand_align_master(1) for each sequential step of a distributed
       alignment  workload.   The  options  to  sand_align_kernel  control  the type of alignment
       (Smith-Waterman, Prefix-Suffix, Banded, etc) and  the  quality  threshhold  for  reporting
       alignments.    These  options  are  typically  passed  in  by  giving  the  -e  option  to
       sand_align_master.

       sand_align_kernel reads a list of sequences from the given input file,  or  from  standard
       input  if  none  is  given.   The sequences are in the compressed fasta format produced by
       sand_compress_reads(1).  The first sequence in the input is compared against all following
       sequences  until a separator line.  Following the separator, the next sequence is compared
       against all following sequences until the following separator, and so on.

OPTIONS

        -a <sw|ps|banded>
              Specify the type of alignment: sw (Smith-Waterman), ps (Prefix-Suffix), or  banded.
              If not specified, default is banded.

        -o <ovl|ovl_new|align|matrix>
              Specify  how  each  alignment  should  be  output:  ovl (Celera V5, V6 OVL format),
              ovl_new (Celera V7 overlap format), align  (display  the  sequences  and  alignment
              graphically)    or    matrix    (display    the    dynamic   programming   matrix).
              sand_align_master(1) expects the ovl output format,  which  is  the  default.   The
              other formats are useful for debugging.

        -m <length>
              Minimum aligment length (default: 0).

        -q <quality>
              Minimum match quality (default: 1.00)

        -x    Delete input file after completion.

        -d <subsystem>
              Enable debugging for this subsystem.  (Try -d all to start.

        -v    Show program version.

        -h    Display this message.

EXIT STATUS

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

EXAMPLES

       Users do not normally invoke sand_align_kernel directly.  Instead, pass arguments by using
       the -e option to sand_align_master(1).  For example, to specify a minimum alignment length
       of 5 and a minimum quality of 0.25:

               % sand_align_master sand_align_kernel -e "-m 5 -q 0.25" mydata.cand mydata.cfa mydata.ovl

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)