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bioRxiv · 10.1101/045690

BIGMAC : Breaking Inaccurate Genomes and Merging Assembled Contigs for long read metagenomic assembly

Ka Kit Lam·Richard Hall·Alicia Clum·Satish Rao
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Abstract

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/increasing N50 and N75. The software is available at https://github.com/kakitone/BIGMAC

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Ka Kit Lam, Richard Hall, Alicia Clum, Satish Rao. 2016-03-29. BIGMAC : Breaking Inaccurate Genomes and Merging Assembled Contigs for long read metagenomic assembly. https://doi.org/10.1101/045690

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