Usage: sga connect [OPTION] ... ASQGFILE BAMFILE Resolve the complete sequence of a paired end fragment by finding a walk through the graph connecting the ends. The graph is read from the ASQGFILE. The reads alignments (to the contigs that make up the graph graph) are read from the BAMFILE. --help display this help and exit -v, --verbose display verbose output -l, --min-distance=LEN minimum expected distance between the PE reads (start to end). Default: 150. -m, --max-distance=LEN maximum expected distance between the PE reads (start to end). This option specifies how long the search should proceed for. Default: 250 -o, --outfile=FILE write the connected reads to FILE --connected-only only write the connected read pairs, not the unresolved vertices in the graph Report bugs to js18@sanger.ac.uk