Usage: sga graph-diff [OPTION] --base BASE.fa --variant VARIANT.fa
Find and report strings only present in the graph of VARIANT when compared to BASE

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -b, --base=FILE                  the baseline reads are in FILE
      -r, --variant=FILE               the variant reads are in FILE
      -o, --outfile=FILE               write the strings found to FILE
      -k, --kmer=K                     use K as the k-mer size for variant discovery
      -x, --kmer-threshold=T           only used kmers seen at least T times
      -y, --max-branches=B             allow the search process to branch B times when 
                                       searching for the completion of a bubble (default: 0)
      -t, --threads=NUM                use NUM computation threads

Report bugs to js18@sanger.ac.uk