AB Small Indel Tool

Description

• 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.

Licensing

• This software is being licensed to you under the OSI compliant GNU Public License (GPL). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this software indicates your acceptance of this licensing agreement. Click on this link to read the licensing agreement.

Support

• This tool is being released as "unsupported software" by Applied Biosystems.

Packages

 Pre-Bioscope™ Tool

• Please contact website support to recieve access information
• The current version of the tool can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here.

Source Distribution (please note that this is a source ONLY distribution of a Bioscope algorithm and available through SVN checkout)

• The current version of the source can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here.