sand_align_kernel - align candidate sequences sequentially
sand_align_kernel [options] [input file]
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
- -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)
- Delete input file after completion.
- -d <subsystem>
- Enable debugging for this subsystem. (Try -d all to start.
- Show program version.
- Display this message.
On success, returns zero. On failure, returns non-zero.
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
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Notre Dame. This software is distributed under the GNU General Public License.
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