Banana Slug Genomics

Usage: sga stats [OPTION] ... READSFILE
Print statistics about the read set. Currently this only prints a histogram
of the k-mer counts

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -p, --prefix=PREFIX              use PREFIX for the names of the index files (default: prefix of the input file)
      -t, --threads=NUM                use NUM threads to compute the overlaps (default: 1)
      -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)
      -k, --kmer-size=N                The length of the kmer to use. (default: 27)
      -n, --num-reads=N                Only use N reads to compute the statistics
      -b, --branch-cutoff=N            stop the overlap search at N branches. This lowers the compute time but will bias the statistics
                                       away from repetitive reads
      --run-lengths                    Print the run length distribution of the BWT
      --kmer-distribution              Print the distribution of kmer counts
      --no-overlap                     Suppress the overlap-based error statistics (faster if you only want the k-mer distribution)

Report bugs to js18@sanger.ac.uk