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