plucky (1) sand_align_kernel.1.gz

Provided by: coop-computing-tools_7.14.5-1_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) 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)