In a previous entry , I mentioned the paper entitled Rare-Allele Detection Using Compressed Se(que)nsing by Noam Shental, Amnon Amir and Or Zuk.Well the project seems to have produced a set of utilities called ComSeq. From the site:
ComSeq is a set of utilities used for simulating and analyzing compressed-sensing pooling design experiments for next-generation sequencing projects. The aim is to identify novel rare alleles, or detect individuals who are carriers of known SNPs in a large population. The package enables an in-silico simulation of a sequencing pooling experiments, including modeling of sequencing error parameters. The package also enables reconstructing genotypes of individuals profiled in real experiments. Detailed instructions and usage examples are given in the README file.
ComSeq is a collaboration between the Broad Institute, the Open University of Israel , and the Weizmann Institute of Science. If you use the package please cite the following paper:
Identification of Rare-Alleles And Their Carriers Using Compressed Se(que)nsing, N. Shental, A. Amir and O. Zuk (2010)
ComSeq includes a set of Matlab functions which can be individually used. You can download the whole package, or individual functions below. To install the package simply download the file comseq.tgz to a directory of your choice, extract it, and add to your Matlab path. The package uses the GPSR algorithm. We thank Mário Figueiredo for allowing us to include it in this package.