TAPyR
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Application data |
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| Created by | Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT |
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| Biological application domain(s) | Whole genome resequencing |
| Principal bioinformatics method(s) | Read mapping |
| Technology | 454, Illumina, Ion Torrent |
| Created at | INESC-ID/IST Lisbon, Portugal |
| Maintained? | Yes |
| Input format(s) | FASTQ, SFF |
| Output format(s) | SAM, BAM |
| Programming language(s) | C |
| Licence | GPL |
Summary: Efficient BWT-based read aligner supporting multiple sequencing platforms
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Description
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 SeqAhead COST action BM1006 "Next Generation Sequencing Data Analysis Network". The complete list of tools developed by the SeqAhead network can be found here.
Links
References
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