Introduction

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.

Publications

  1. BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.
    Cite this
    Lam KK, Hall R, Clum A, Rao S, 2016-10-01 - BMC Bioinformatics

Credits

  1. Ka-Kit Lam
    Developer

    Department of Electrical Engineering and Computer Sciences, UC Berkeley, United States of America

  2. Richard Hall
    Developer

    -, Pacific Biosciences, United States of America

  3. Alicia Clum
    Developer

    Joint Genome Institute, Walnut Creek, United States of America

  4. Satish Rao
    Investigator

    Department of Electrical Engineering and Computer Sciences, UC Berkeley, United States of America

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Summary
AccessionBT000202
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted BySatish Rao