Aggressive Assembly of Pyrosequencing Reads With Mates

. 2008 Dec 15;24(24):2818-24.

doi: 10.1093/bioinformatics/btn548. Epub 2008 October 24.

Aggressive assembly of pyrosequencing reads with mates

Affiliations

PMID: 18952627
PMCID: PMC2639302
DOI: 10.1093/bioinformatics/btn548

Free PMC article

Aggressive associates of pyrosequencing reads with mates

Jason R Miller et al. Bioinformatics. 2008 .

Free PMC article

Abstract

Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in toll, accuracy, typical coverage, boilerplate read length and the variety of available paired-end protocols. Both read types tin can complement 1 another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must exist modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.

Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length doubt, loftier read coverage and heterogeneous read lengths. In tests on iv genomes, it generated the longest contigs amid all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-associates was detected in some CABOG assemblies, just this was reduced in the presence of sufficient mate pair data.

Availability: The software is freely bachelor equally open-source from http://wgs-assembler.sf.net nether the GNU Public License.

Figures

Fig. 1. — **Fig. ane.**
Two representations of a best overlap graph. In (a), the layout resembles a multiple sequence alignment. In (b) each read is represented by two nodes joined by an undirected border. Arrows represent all-time overlaps, where best means covering the most sequence. There are common best overlaps between successive pairs of reads A through D. Due to erroneous bases at one end (wavy line), read E has a non-mutual best overlap to B. Paths span undirected and directed edges alternately. Path EBA converges on path ABCD. CABOG scores read E lower than the others since only iii reads are on paths from it. Starting with whatever one of the loftier-scoring reads, CABOG would build initial unitig ABCD, and then E. Using saved information nigh each path intersection, CABOG would discount the intersection at B because the path from Due east spanned merely one read earlier B. Information technology would pause ABCD only if at that place were also a change in read arrival rate at B, which is not the case here. Although linear-time directed-path following finds the longest possible unitig in this constructed case, it is non guaranteed to do so when paths bridge multiple intersections.

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Aggressive Assembly of Pyrosequencing Reads With Mates