An evaluation of the accuracy and speed of metagenome analysis tools

Scientific Reports
Stinus LindgreenPaul P Gardner

Abstract

Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 2, 1998·Bioinformatics·J StoyeF Meyer
Apr 5, 2002·Genome Research·W James Kent
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Aug 6, 2005·Science·Jay ShendureGeorge M Church
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Oct 15, 2008·Genome Biology·Martin Wu, Jonathan A Eisen
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Feb 11, 2010·BMC Bioinformatics·Martin C FrithPaul Horton
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Aug 17, 2010·Bioinformatics·Robert C Edgar
Sep 2, 2010·Nucleic Acids Research·Mina RhoYuzhen Ye
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Aug 25, 2011·Nature Reviews. Rheumatology·Jose U Scher, Steven B Abramson
Sep 2, 2011·Nature·Vanessa M D'CostaGerard D Wright
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Nov 15, 2011·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Nov 19, 2011·Nucleic Acids Research·Sarah HunterSiew-Yit Yong
Dec 1, 2011·Nucleic Acids Research·Marco PuntaRobert D Finn
Dec 27, 2011·Bioinformatics·Weichun HuangGabor T Marth
Feb 24, 2012·Journal of Basic Microbiology·Qiangde DuanGuoqiang Zhu
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Aug 29, 2012·PloS One·Colin F DavenportFrauke Sprengel
Nov 20, 2012·Nucleic Acids Research·Christian J A SigristIoannis Xenarios
Dec 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·Noah FiererJ Gregory Caporaso
Dec 20, 2012·PloS One·Raul Y TitoCecil M Lewis
Feb 7, 2013·Trends in Neurosciences·Jane A Foster, Karen-Anne McVey Neufeld
Feb 13, 2013·Clinical Chemistry·Sridevi DevarajJames Versalovic
Mar 22, 2013·Genome Announcements·Sulbha ChoudhariAndrey Grigoriev
Jul 6, 2013·Bioinformatics·Sasha K AmesJonathan E Allen
Aug 27, 2013·Nature Biotechnology·Morgan G I LangilleCurtis Huttenhower

❮ Previous
Next ❯

Citations

Oct 11, 2015·Bioinformatics·Genivaldo Gueiros Z SilvaRobert A Edwards
Apr 14, 2016·Nature Communications·Peter MenzelAnders Krogh
May 7, 2016·Bioinformatics·Vitor C PiroBernhard Y Renard
May 11, 2016·FEMS Microbiology Ecology·Richard J Randle-BoggisPeter D Ashton
Aug 20, 2016·Bioinformatics·Rachid Ounit, Stefano Lonardi
Jan 27, 2017·Microorganisms·Sulbha Choudhari, Andrey Grigoriev
Jan 27, 2017·Annual Review of Food Science and Technology·Aaron M WalshPaul D Cotter
Apr 4, 2017·The New Phytologist·Laura ParducciMikkel Winther Pedersen
Jan 5, 2018·Genes·Sandra Christine Andersen, Jeffrey Hoorfar
Mar 29, 2018·Algorithms for Molecular Biology : AMB·Samuele GirottoCinzia Pizzi
Dec 7, 2017·Bioinformatics·Askarbek N OrakovIgor I Goryanin
Apr 17, 2018·PLoS Computational Biology·Mark Reppell, John Novembre
Nov 10, 2017·Journal of Clinical Microbiology·Jie LiuEric Houpt
Sep 30, 2017·Bioinformatics·André MüllerBertil Schmidt
Jan 18, 2018·Nature Ecology & Evolution·Åshild J VågeneJohannes Krause
Jan 17, 2019·Bioinformatics·Subrata SahaSanguthevar Rajasekaran
Mar 21, 2018·Genes & Nutrition·Bastian HornungPeter J Schaap
Oct 3, 2017·Nature Methods·Alexander SczyrbaAlice C McHardy
May 2, 2017·Annual Review of Genomics and Human Genetics·Christina WarinnerJohannes Krause
Sep 25, 2017·Genome Biology·Alexa B R McIntyreChristopher E Mason
Apr 18, 2019·Bioinformatics·Gregory Kucherov
Aug 10, 2017·Nature Reviews. Gastroenterology & Hepatology·Marcus J ClaessonPaul W O'Toole
Oct 3, 2019·Extremophiles : Life Under Extreme Conditions·Ammar AlibrahimMaria Dittrich
Nov 12, 2019·Frontiers in Plant Science·Rares LucaciuThomas Rattei
Dec 18, 2019·Clinical Chemistry·Robert Schlaberg
Feb 16, 2020·Digestive Diseases and Sciences·Cade EmletRegina Lamendella
Mar 29, 2019·Nature Communications·Serghei MangulJonathan Flint
Jun 20, 2017·Applied and Environmental Microbiology·Aaron M WalshPaul D Cotter
Jul 6, 2019·BMJ Open Ophthalmology·Davide BorroniStefano Ferrari

❮ Previous
Next ❯

Methods Mentioned

BETA
amplicon sequencing

Software Mentioned

BLASTN
LAST
LMAT
BLAT
tk
Bowtie
Diamond
BLASTX
BioPython
GOTTCHA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

International Journal of Food Microbiology
Gilles KergourlayMarie-Christine Champomier Vergès
Nature Methods
Johannes AlnebergChristopher Quince
© 2022 Meta ULC. All rights reserved