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