Usage: sga metagenome [OPTION] READS
Assemble contigs from the metagenomics data in READS

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -k, --kmer=K                     use a k-mer size of size K
      -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)
      -o, --outfile=FILE               write contigs to FILE (default: contigs.fa)

Report bugs to js18@sanger.ac.uk