NAME

       sga-bam2de - Make a distance estimate file from a bam file of reads aligned to contigs

DESCRIPTION

       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.