New approaches for metagenome assembly with short reads

被引：118

作者：

Ayling, Martin ^{[1
]}

Clark, Matthew D. ^{[2
]}

Leggett, Richard M. ^{[1
]}

机构：

[1] Earlham Inst, Norwich Res Pk, Norwich, Norfolk, England

[2] Nat Hist Museum, Life Sci, London, England

来源：

BRIEFINGS IN BIOINFORMATICS | 2020年 / 21卷 / 02期

基金：

英国生物技术与生命科学研究理事会;

关键词：

Metagenomics; assembly; algorithms; sequencing; DE-NOVO ASSEMBLER; SINGLE-CELL; GENOME; CONTIGS; DIVERSITY; COVERAGE; VIRUSES;

D O I：

10.1093/bib/bbz020

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 data sets, 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.

引用

页码：584 / 594

页数：11