September 22, 2019  |  

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

Authors: Lam, Ka-Kit and Hall, Richard and Clum, Alicia and Rao, Satish

The 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.Using 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. BIGMAC demonstrates the effectiveness of the post-processing approach in improving the quality of metagenomic assemblies.

Journal: BMC bioinformatics
DOI: 10.1186/s12859-016-1288-y
Year: 2016

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