RT Journal Article
SR Electronic
T1 BIGMAC: Breaking Inaccurate Genomes and Merging Assembled Contigs for long read metagenomic assembly
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 045690
DO 10.1101/045690
A1 Ka-Kit Lam
A1 Richard Hall
A1 Alicia Clum
A1 Satish Rao
YR 2016
UL http://biorxiv.org/content/early/2016/03/29/045690.abstract
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