New approaches for assembly of short-read metagenomic data

Earlham Institute, Norwich, UK
Natural History Museum, London, UK
Subject Areas
Bioinformatics, Genomics
Metagenomics, assembly, algorithms, sequencing
© 2018 Ayling et al.
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Ayling M, Clark MD, Leggett RM. 2018. New approaches for assembly of short-read metagenomic data. PeerJ Preprints 6:e27332v1


In recent years, the use of longer-range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic datasets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.

Author Comment

This is a preprint submission to PeerJ Preprints.