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)