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Short description:
Please summarise the application in a few sentences. Avoid links here. Compute enhanced suffix array
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Genome indexing (suffix arrays)
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
This enhanced suffix array requires 5 n bytes of memory, where n is the length of the input sequence <pre> 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>. </pre>
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