Suffixerator

Application data
Created by	Kurtz S
Principal bioinformatics method(s)	Genome indexing (suffix arrays)
Maintained?	Maybe
Input format(s)	FASTA, fasta.gz
Software features	Part of GenomeTools
Operating system(s)	Linux

Summary: Compute enhanced suffix array

"Error: no local variable "counter" was set." is not a number.

This enhanced suffix array requires 5 n bytes of memory, where n is the length of the input sequence

gt suffixerator -help
Usage: /sw/bin/gt suffixerator [option ...] (-db file [...] | -ii index)
Compute enhanced suffix array.

-db           specify database files
-ii           specify sequence index created previously by -tis option
              default: undefined
-smap         specify file containing a symbol mapping
              default: undefined
-dna          input is DNA sequence
              default: no
-protein      input is Protein sequence
              default: no
-plain        process as plain text
              default: no
-dir          specify reading direction (fwd, cpl, rev, rcl)
              default: fwd
-indexname    specify name for index to be generated
              default: undefined
-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
-sat          specify kind of sequence representation
              default: undefined
-tis          output transformed and encoded input sequence to file
              default: no
-ssp          output sequence separator positions to file
              default: no
-des          output sequence descriptions to file
              default: no
-sds          output sequence description separator positions to file
              default: no
-kys          output/sort according to keys of the form |key| in fasta header
              default: nosort
-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
-showtime     show the time of the different computation phases
              default: no
-showprogress show a progress bar
              default: no
-v            be verbose 
              default: no
-help         display help and exit
-version      display version information and exit

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

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