BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

BMC Bioinformatics

Research Article

Satish Rao¹  Ka-Kit Lam¹  Alicia Clum²  Richard Hall³ 

[1] Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, USA;Joint Genome Institute, Walnut Creek, USA;Pacific Biosciences, Menlo Park, USA;

关键词: Genome assembly;    Next generation sequencing;    Metagenomics;   

DOI  :  10.1186/s12859-016-1288-y

 received in 2016-04-14, accepted in 2016-09-29,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement. Previous approaches have focused on pre-processing reads and optimizing assemblers. BIGMAC takes an alternative perspective to focus on the post-processing step.ResultsUsing both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subsequently scaffolds contigs. Our experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality by reducing the number of mis-assemblies while maintaining or increasing N50 and N75. Moreover, BIGMAC shows the largest N75 to number of mis-assemblies ratio on all tested datasets when compared to other post-processing tools.ConclusionsBIGMAC demonstrates the effectiveness of the post-processing approach in improving the quality of metagenomic assemblies.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

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