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<code> [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 </code>
