RA Tools for Resequencing Arrays
RA Tools provides a rigorous framework for the analysis of resequencing microarrays. RA Tools is being released as part of the DPGP project to provide open source tools for resequencing and population genomics.
RA Tools consists of three modules:
- RA GridAlign: Performs a locally perfect grid alignment. Now works with any Affymetrix or Nimblegen resequencing array.
- RA BaseCaller: Uses a maximum likelyhood approach for calling bases. It is independent of underlying chip architecture and can be run on any properly formatted data. It has been tested with resequencing arrays from Affymetrix and Nimblegen.
- RA Final: Corrects for various data artifacts as described in Cutler et al.
- Download Version 1.0.5
- Download Version 1.0.6 [requires libtiff]
The most current documentation on compiling and using RA Tools is available here:
The algorithm for base calling is published in the following reference:
High-throughput variation detection and genotyping using microarrays.
Cutler DJ, Zwick ME, Carrasquillo MM, Yohn CT, Tobin KP, Kashuk C, Mathews DJ, Shah NA, Eichler EE, Warrington JA, Chakravarti A.
Genome Res. 2001 Nov;11(11):1913-25.
The latest sourcecode is available at the
DPGP Anonymous CVS
Developer documentation for the repository
DPGP WIKI: Developer Access to CVS