Usage: sga assemble [OPTION] ... ASQGFILE Create contigs from the assembly graph ASQGFILE. -v, --verbose display verbose output --help display this help and exit -o, --out-prefix=NAME use NAME as the prefix of the output files (output files will be NAME-contigs.fa, etc) -m, --min-overlap=LEN only use overlaps of at least LEN. This can be used to filter the overlap set so that the overlap step only needs to be run once. Bubble/Variation removal parameters: -b, --bubble=N perform N bubble removal steps (default: 3) -d, --max-divergence=F only remove variation if the divergence between sequences is less than F (default: 0.05) -g, --max-gap-divergence=F only remove variation if the divergence between sequences when only counting indels is less than F (default: 0.01) Setting this to 0.0 will suppress removing indel variation --max-indel=D do not remove variation that is an indel of length greater than D (default: 20) Trimming parameters: -x, --cut-terminal=N cut off terminal branches in N rounds (default: 10) -l, --min-branch-length=LEN remove terminal branches only if they are less than LEN bases in length (default: 150) Small repeat resolution parameters: -r,--resolve-small=LEN resolve small repeats using spanning overlaps when the difference between the shortest and longest overlap is greater than LEN (default: not performed) Report bugs to js18@sanger.ac.uk