New approaches for metagenome assembly with short reads.

Briefings in Bioinformatics
Martin AylingRichard M Leggett

Abstract

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.

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Citations

Dec 19, 2019·Briefings in Bioinformatics·Richa Bharti, Dominik G Grimm
Feb 1, 2020·Digestive Diseases and Sciences·Jessica Galloway-Peña, Blake Hanson
Aug 5, 2020·Journal, Genetic Engineering & Biotechnology·Fitra Adi PrayogoNurhayati Nurhayati
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Aug 15, 2020·Genome Medicine·Yan YanCurtis Huttenhower
Aug 23, 2020·Genes·Quang Tran, Vinhthuy Phan
Dec 12, 2020·Frontiers in Microbiology·Krisztián LacziKatalin Perei
Mar 11, 2021·MBio·Marija DmitrijevaChristian von Mering
Mar 25, 2021·Briefings in Bioinformatics·Masood Ur Rehman KayaniLei Chen
Apr 10, 2021·Frontiers in Microbiology·Alla L Lapidus, Anton I Korobeynikov
May 8, 2021·PLoS Computational Biology·Lauren M LuiAdam P Arkin
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Feb 1, 2022·Critical Reviews in Microbiology·Paton VuongParwinder Kaur

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Methods Mentioned

BETA
HiC

Software Mentioned

MetaGTA
SOAPdenovo
EnsembleAssembler
InteMAP
MetaCRAM
Canu
BLAST
MetaVelvet
Ray Meta
dBg

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