PT  - JOURNAL ARTICLE
AU  - Ka-Kit Lam
AU  - Richard Hall
AU  - Alicia Clum
AU  - Satish Rao
TI  - BIGMAC: Breaking Inaccurate Genomes and Merging Assembled Contigs for long read metagenomic assembly
AID  - 10.1101/045690
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 045690
4099  - http://biorxiv.org/content/early/2016/03/29/045690.short
4100  - http://biorxiv.org/content/early/2016/03/29/045690.full
AB  - 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