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) 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)