$ sga overlap --help Usage: sga overlap [OPTION] ... READSFILE Compute pairwise overlap between all the sequences in READS --help display this help and exit -v, --verbose display verbose output -t, --threads=NUM use NUM worker threads to compute the overlaps (default: no threading) -e, --error-rate the maximum error rate allowed to consider two sequences aligned (default: exact matches only) -m, --min-overlap=LEN minimum overlap required between two reads (default: 45) -p, --prefix=PREFIX use PREFIX for the names of the index files (default: prefix of the input file) -f, --target-file=FILE perform the overlap queries against the reads in FILE -x, --exhaustive output all overlaps, including transitive edges --exact force the use of the exact-mode irreducible block algorithm. This is faster but requires that no substrings are present in the input set. -l, --seed-length=LEN force the seed length to be LEN. By default, the seed length in the overlap step is calculated to guarantee all overlaps with --error-rate differences are found. This option removes the guarantee but will be (much) faster. As SGA can tolerate some missing edges, this option may be preferable for some data sets. -s, --seed-stride=LEN force the seed stride to be LEN. This parameter will be ignored unless --seed-length is specified (see above). This parameter defaults to the same value as --seed-length -d, --sample-rate=N sample the symbol counts every N symbols in the FM-index. Higher values use significantly less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) Report bugs to js18@sanger.ac.uk