GT-SUFFIXERATOR(1)

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>.