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

Authors:
Brian D. Ondov;Anjana Varadarajan;Karla D. Passalacqua;Nicholas H. Bergman
Affiliations:
-;-;-;-
Venue:
Bioinformatics
Year:
2008

Citing 0
Cited 1

Seed design framework for mapping SOLiD reads

RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology

Quantified Score

Hi-index	3.84

Visualization

Abstract

Summary: 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/ Contact: nickbergman@gatech.edu Supplementary information:Supplementary data are available at Bioinformatics Online.