sand_align_kernel1

Usage

Overview

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