Usage: sga cluster [OPTION] READS Extract clusters of reads belonging to the same connected components. -v, --verbose display verbose output --help display this help and exit -o, --out=FILE write the clusters to FILE (default: clusters.txt) -c, --min-cluster-size=N only write clusters with at least N reads (default: 2) -x, --max-cluster-size=N abort the search if the cluster size exceeds N -m, --min-overlap=N require an overlap of at least N bases between reads (default: 45) -e, --error-rate the maximum error rate allowed to consider two sequences aligned (default: exact matches only) -t, --threads=NUM use NUM worker threads to compute the overlaps (default: no threading) --extend=FILE extend previously existing clusters in FILE Report bugs to js18@sanger.ac.uk