Banana Slug Genomics

$ 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