MetaQUAST: evaluation of metagenome assemblies
TLDR
MetaQUAST is presented, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference, and addresses such metagenome datasets features as unknown species content by detecting and downloading reference sequences.Abstract:
Summary: During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets. Availability and implementation: http://bioinf.spbau.ru/metaquast. Contact: aleksey.gurevich@spbu.ru Supplementary information: Supplementary data are available at Bioinformatics online.read more
Citations
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
MetaSPAdes: A new versatile metagenomic assembler
TL;DR: MetaSPAdes as mentioned in this paper addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes.
Journal ArticleDOI
Using SPAdes De Novo Assembler
TL;DR: Protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets are presented.
Journal ArticleDOI
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics.
Juan Jovel,Jordan Patterson,Weiwei Wang,Naomi Hotte,Sandra O'Keefe,Troy Mitchel,Troy Perry,Dina Kao,Andrew Mason,Karen L. Madsen,Gane Ka-Shu Wong +10 more
TL;DR: The two main approaches for analyzing the microbiome, 16S ribosomal RNA gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses and several methods for taxonomic classification of bacterial sequences are discussed.
Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
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