focal (1) sand_align_kernel.1.gz

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

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


       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)