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.
| -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. |
% sand_align_master sand_align_kernel -e "-m 5 -q 0.25" mydata.cand mydata.cfa mydata.ovl