Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.

ABSTRACT:

Unlabelled

Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq.

Availability

Executables, source code, and sample data are available at http://socs.biology.gatech.edu/

SUBMITTER: Ondov BD 

PROVIDER: S-EPMC2639273 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature