Campus Units

Computer Science

Document Type

Book Chapter

Publication Version

Accepted Manuscript

Publication Date

2017

Journal or Book Title

Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution

First Page

35

Last Page

45

DOI

10.1007/978-1-4939-6622-6_2

Abstract

We describe an efficient method for assembling short reads into long sequences. In this method, a hashing technique is used to compute overlaps between short reads, allowing base mismatches in the overlaps. Then an overlap graph is constructed, with each vertex representing a read and each edge representing an overlap. The overlap graph is explored by graph algorithms to find unique paths of reads representing contigs. The consensus sequence of each contig is constructed by computing alignments of multiple reads without gaps. This strategy has been implemented as a short read assembly program called PCAP.Solexa. We also describe how to use PCAP. Solexa in assembly of short reads.

Comments

This is a manuscript of a chapter published as Huang X. (2017) Sequence Assembly. In: Keith J. (eds) Bioinformatics: Volume 1: Data, Sequence Analysis, and Evolution. Humana Press, New York, NY. doi: 10.1007/978-1-4939-6622-6_2. Posted with permission.

Copyright Owner

Springer Science+Business Media New York

Language

en

File Format

application/pdf

Published Version

Share

COinS