[jolespin@campusrocks2 bin]$ ./sga fm-merge --help
Usage: sga fm-merge [OPTION] ... READSFILE
Merge unambiguously sequences from the READSFILE using the FM-index.
This program requires rmdup to be run before it.

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -p, --prefix=PREFIX              use PREFIX for the names of the index files (default: prefix of the input file)
      -t, --threads=NUM                use NUM worker threads (default: no threading)
      -m, --min-overlap=LEN            minimum overlap required between two reads to merge (default: 45)
      -o, --outfile=FILE               write the merged sequences to FILE (default: basename.merged.fa)

Report bugs to js18@sanger.ac.uk