sga-bam2de - Make a distance estimate file from a bam file of
reads aligned to contigs
sga-bam2de.pl - Make a distance estimate file from a bam file of
reads aligned to contigs sga-bam2de.pl -n N --prefix lib300
lib300.bam Options:
- -n N
- Minimum number of pairs required to consider two contigs linked
- -m LEN
- Only find links between contigs with length at least LEN bp (default:
200)
- -t NUM
- Use NUM threads for computing the distance estimates
- --prefix
NAME
- Use NAME as the prefix for the outfiles
- --mind D
- Set the minimum distance estimate to test to be D. This should be a
negative number if contigs are expected to overlap. Defaults to
-99bp.
- --mina N
- Set the minimum alignment length to be N.
- --help
- This help output.