Banana Slug Genomics

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Usage: sga index [OPTION] ... READSFILE
Index the reads in READSFILE using a suffixarray/bwt

  -v, --verbose                        display verbose output
      --help                           display this help and exit
  -a, --algorithm=STR                  BWT construction algorithm. STR can be:
                                       sais - induced sort algorithm, slower but works for very long sequences (default)
                                       ropebwt - very fast and memory efficient. use this for short (<200bp) reads
  -d, --disk=NUM                       use disk-based BWT construction algorithm. The suffix array/BWT will be constructed
                                       for batchs of NUM reads at a time. To construct the suffix array of 200 megabases of sequence
                                       requires ~2GB of memory, set this parameter accordingly.
  -t, --threads=NUM                    use NUM threads to construct the index (default: 1)
  -c, --check                          validate that the suffix array/bwt is correct
  -p, --prefix=PREFIX                  write index to file using PREFIX instead of prefix of READSFILE
      --no-reverse                     suppress construction of the reverse BWT. Use this option when building the index
                                       for reads that will be error corrected using the k-mer corrector, which only needs the forward index
      --no-forward                     suppress construction of the forward BWT. Use this option when building the forward and reverse index separately
      --no-sai                         suppress construction of the SAI file. This option only applies to -a ropebwt
  -g, --gap-array=N                    use N bits of storage for each element of the gap array. Acceptable values are 4,8,16 or 32. Lower
                                       values can substantially reduce the amount of memory required at the cost of less predictable memory usage.
                                       When this value is set to 32, the memory requirement is essentially deterministic and requires ~5N bytes where
                                       N is the size of the FM-index of READS2.
                                       The default value is 8.

Report bugs to js18@sanger.ac.uk
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Banana Slug Genomics

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