Campus Units

Computer Science

Document Type

Article

Publication Version

Published Version

Publication Date

2006

Journal or Book Title

Genome Research

Volume

16

First Page

768

Last Page

775

DOI

10.1101/gr.5090606

Abstract

We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical maps. Clone sizes and overlaps derived from clone fingerprints are used for the calculation of length constraints between any two BAC neighbors sharing 40% of their size. These constraints are used to promote the linkage and guide the arrangement of sequence contigs within a sequence scaffold at the layout phase of WGS assemblies. This process is facilitated by FASSI, a stand-alone application that calculates BAC end and BAC overlap length constraints from clone fingerprint map contigs created by the FPC package. FASSI is designed to work with the assembly tool PCAP, but its output can be formatted to work with other WGS assembly algorithms able to use length constraints for individual clones. The FASSI method is simple to implement, potentially cost-effective, and has resulted in the increase of scaffold contiguity for both the Drosophila melanogaster and Cryptococcus gattii genomes when compared to a control assembly without map-derived constraints. A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity.

Comments

This article is published as Warren, René L., Dmitry Varabei, Darren Platt, Xiaoqiu Huang, David Messina, Shiaw-Pyng Yang, James W. Kronstad et al. "Physical map-assisted whole-genome shotgun sequence assemblies." Genome Research 16 (2006): 768-775. doi: 10.1101/gr.5090606.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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