AB Small Indel Tool
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Application data |
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| Created by | ABI |
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| Biological application domain(s) | Indel detection, Sequencing |
| Principal bioinformatics method(s) | Read mapping, Sequence alignment |
| Technology | ABI SOLiD |
| Created at | ABI |
| Maintained? | Maybe |
| Input format(s) | PAS |
| Output format(s) | GFF |
| Programming language(s) | Perl, C++ |
| Licence | GPL |
| Operating system(s) | Linux 64 |
Summary: The SOLiD™ Small Indel Tool processes the indel evidences found in the pairing step of the SOLiD™ System Analysis pipeline Tool (Corona Lite).
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The SOLiD™ Small Indel Tool processes the indel evidences found in the pairing step of the SOLiD™ System Analysis pipeline Tool (Corona Lite). In the pairing pipeline, these evidences are found in mate pairs by using the placement of one tag such that the other tag can be used to search for the presence of a small indel. Specifically, all placements of the ends of the read within a good pairing distance of the placed tag, form an alignment when the ends are successfully joined together to form a gapped alignment with either an insertion or deletion within a size specified in the pairing pipeline. This tool processes these results further by combining evidences together based on proximity to form candidates. Once these combined results are formed, the tool allows for the combination of several runs together, and for filtering based on the average read position of the indel and number of non-redundant reads. The tool also allows for easy downstream analysis by producing the candidates in a text format useful for importing into databases and in a public GFF version 3 format.
Links
- AB Small Indel Tool Homepage [ edit link ]
- AB Small Indel Tool Manual [ edit link ]
- AB Small Indel Tool Manual [ edit link ]
References
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