NAME

       sawriter - generate suffix arrays for nucleotide sequences

SYNOPSIS

       sawriter saOut  fastaIn [fastaIn2 fastaIn3 ...]  [-blt p] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter]

       sawriter fastaIn (writes to fastaIn.sa)

OPTIONS

       -blt p Build  a  lookup table on prefixes of length p. This speeds up lookups considerably (more than the
              LCP table), but misses matches less than p when searching.

       -4bit  Read in (one) fasta file as a compressed sequence file.

       Methods
              -larsson (default)  Uses the method of Larsson and Sadakane to build the array.

              -mamy  Uses the method of MAnber and MYers to build the array (slower than larsson,  and  produces
                     the same result. This is mainly for double checking the correctness of larsson).

              -kark  Use Karkkainen DS3 method for building the suffix array.  This will probably be slower than
                     larsson, but takes only an extra N/(sqrt 3) extra space.

              -mafe  (disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina

              -welter
                     Use  lightweight  (sort  of light) suffix array construction.  This is a bit more slow than
                     normal larsson.

       -welterweight N
              use a difference cover of size N for building the suffix array.  Valid values are 7,32,64,111, and
              2281.

SEE ALSO

       blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1) samtom4(1) sdpMatcher(1) toAfg(1)

sawriter 3ca7fe8                                    July 2015                                        SAWRITER(1)