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Short description:
Please summarise the application in a few sentences. Avoid links here. Efficient BWT-based read aligner supporting multiple sequencing platforms
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Whole genome resequencing,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
454, Illumina, 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):
INESC-ID/IST Lisbon, Portugal
== Description == <!-- Describe the application in the space below --> TAPyR is a read mapper supporting data from multiple sequencing platforms, including Roche 454 GS FLX, Life Technologies Ion Torrent, Illumina HiSeq, etc. It supports both single and paired-end reads, and complies to IO file standards, taking inputs in FASTAQ and SFF formats, and generating SAM files as output. TAPyR uses a custom BWT-based indexing strategy coupled with a seed-and-extend heuristic. The applicaiton has moderate main memory requirements (roughly 1.6x the size of the reference sequence) and has displayed class-leading CPU performance in our tests. The use of the tool is straightforward, requiring minimum user parameterization. TAPyR team participates in the [http://www.seqahead.eu/ SeqAhead] COST action BM1006 "Next Generation Sequencing Data Analysis Network". The complete list of tools developed by the SeqAhead network can be found [http://seqahead.cs.tu-dortmund.de/wgs:wg3:start here]. <!-- -->
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