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