Scroll to navigation

SGA-BAM2DE(1) User Commands SGA-BAM2DE(1)

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.
June 2016 sga-bam2de 0.10.14