NAME

       gt-suffixerator - Compute enhanced suffix array.

SYNOPSIS

       gt suffixerator [option ...] (-db file [...] | -ii index)

OPTIONS

       -ssp
           output sequence separator positions to file (default: yes)

       -des
           output sequence descriptions to file (default: yes)

       -sds
           output sequence description separator positions to file (default: yes)

       -md5
           output MD5 sums to file (default: yes)

       -sat
           specify kind of sequence representation by one of the keywords direct, bytecompress,
           eqlen, bit, uchar, ushort, uint32 (default: undefined)

       -dna
           input is DNA sequence (default: no)

       -protein
           input is protein sequence (default: no)

       -indexname
           specify name for index to be generated (default: undefined)

       -db
           specify database files

       -smap
           specify file containing a symbol mapping (default: undefined)

       -lossless
           allow lossless original sequence retrieval (default: no)

       -mirrored
           virtually append the reverse complement of each sequence (default: no)

       -pl
           specify prefix length for bucket sort recommendation: use without argument; then a
           reasonable prefix length is automatically determined. (default: 0)

       -dc
           specify difference cover value (default: 0)

       -spmopt
           optimize esa-construction for suffix-prefix matching (default: 0)

       -memlimit
           specify maximal amount of memory to be used during index construction (in bytes, the
           keywords MB and GB are allowed) (default: undefined)

       -kys
           output/sort according to keys of the form |key| in fasta header (default: nosort)

       -dir
           specify reading direction (fwd, cpl, rev, rcl) (default: fwd)

       -suf
           output suffix array (suftab) to file (default: no)

       -lcp
           output lcp table (lcptab) to file (default: no)

       -bwt
           output Burrows-Wheeler Transformation (bwttab) to file (default: no)

       -bck
           output bucket table to file (default: no)

       -v
           be verbose (default: no)

       -showprogress
           show a progress bar (default: no)

       -ii
           specify existing encoded sequence (default: undefined)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

AUTHOR

       Report bugs to <kurtz@zbh.uni-hamburg.de>.

                                            10/07/2012                         GT-SUFFIXERATOR(1)