Usage: sga gapfill [OPTION] SCAFFOLDS.fa Fill in scaffold gaps using walks through a de Bruijn graph --help display this help and exit -v, --verbose display verbose output -p, --prefix=NAME load the FM-index with prefix NAME -s, --start-kmer=K First kmer size used to attempt to resolve each gap (default: 91) -e, --end-kmer=K Last kmer size used to attempt to resolve each gap (default: 51) -x, --kmer-threshold=T only use kmers seen at least T times -t, --threads=NUM use NUM computation threads -d, --sample-rate=N use occurrence array sample rate of N in the FM-index. Higher values use significantly less memory at the cost of higher runtime. This value must be a power of 2 (default: 128) Report bugs to js18@sanger.ac.uk