sand_align_kernel(1)

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) 2005-2011 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)

  • CCTools 4.1.4rc5 released on 04/10/2014