PANDAseq: paired-end assembler for illumina sequences

BMC Bioinformatics

Software

Jakub M Truszkowski¹  Daniel G Brown¹  Josh D Neufeld²  Andre P Masella²  Andrea K Bartram² 

[1] David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada;Department of Biology, University of Waterloo, Waterloo, Ontario, Canada;

关键词: Quality Score;    Quality Threshold;    Base Match;    Control Library;    High Quality Score;   

DOI  :  10.1186/1471-2105-13-31

 received in 2011-09-23, accepted in 2012-02-14,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundIllumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.ResultsPANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods.ConclusionsPANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.

【 授权许可】

Unknown   
© Masella et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.