Literature DB >> 25218180

Binning metagenomic contigs by coverage and composition.

Johannes Alneberg1, Brynjar Smári Bjarnason1, Ino de Bruijn2, Melanie Schirmer3, Joshua Quick4, Umer Z Ijaz3, Leo Lahti5, Nicholas J Loman6, Anders F Andersson1, Christopher Quince7.   

Abstract

Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

Entities:  

Mesh：

Year:  2014        PMID： 25218180     DOI： 10.1038/nmeth.3103

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  17 in total

1.  Community structure and metabolism through reconstruction of microbial genomes from the environment.

Authors:  Gene W Tyson; Jarrod Chapman; Philip Hugenholtz; Eric E Allen; Rachna J Ram; Paul M Richardson; Victor V Solovyev; Edward M Rubin; Daniel S Rokhsar; Jillian F Banfield
Journal:  Nature       Date:  2004-02-01       Impact factor: 49.962

Review 2.  A genomic perspective on protein families.

Authors:  R L Tatusov; E V Koonin; D J Lipman
Journal:  Science       Date:  1997-10-24       Impact factor: 47.728

3.  Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.

Authors:  Jason Pell; Arend Hintze; Rosangela Canino-Koning; Adina Howe; James M Tiedje; C Titus Brown
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-30       Impact factor: 11.205

4.  Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.

Authors:  R Sandberg; G Winberg; C I Bränden; A Kaske; I Ernberg; J Cöster
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

5.  Ray Meta: scalable de novo metagenome assembly and profiling.

Authors:  Sébastien Boisvert; Frédéric Raymond; Elénie Godzaridis; François Laviolette; Jacques Corbeil
Journal:  Genome Biol       Date:  2012-12-22       Impact factor: 13.583

6.  Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.

Authors:  Itai Sharon; Michael J Morowitz; Brian C Thomas; Elizabeth K Costello; David A Relman; Jillian F Banfield
Journal:  Genome Res       Date:  2012-08-30       Impact factor: 9.043

7.  Structure, function and diversity of the healthy human microbiome.

Authors: 
Journal:  Nature       Date:  2012-06-13       Impact factor: 49.962

8.  The binning of metagenomic contigs for microbial physiology of mixed cultures.

Authors:  Marc Strous; Beate Kraft; Regina Bisdorf; Halina E Tegetmeyer
Journal:  Front Microbiol       Date:  2012-12-05       Impact factor: 5.640

9.  Unsupervised statistical clustering of environmental shotgun sequences.

Authors:  Andrey Kislyuk; Srijak Bhatnagar; Jonathan Dushoff; Joshua S Weitz
Journal:  BMC Bioinformatics       Date:  2009-10-02       Impact factor: 3.169

10.  Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.

Authors:  Daniel P R Herlemann; Daniel Lundin; Matthias Labrenz; Klaus Jürgens; Zongli Zheng; Henrik Aspeborg; Anders F Andersson
Journal:  MBio       Date:  2013-05-28       Impact factor: 7.867
View more
  501 in total

1.  Strain recovery from metagenomes.

Authors:  C Titus Brown
Journal:  Nat Biotechnol       Date:  2015-10       Impact factor: 54.908

2.  Metabolic network-guided binning of metagenomic sequence fragments.

Authors:  Matthew B Biggs; Jason A Papin
Journal:  Bioinformatics       Date:  2015-11-14       Impact factor: 6.937

3.  Galacturonate Metabolism in Anaerobic Chemostat Enrichment Cultures: Combined Fermentation and Acetogenesis by the Dominant sp. nov. "Candidatus Galacturonibacter soehngenii".

Authors:  Laura C Valk; Jeroen Frank; Pilar de la Torre-Cortés; Max van 't Hof; Antonius J A van Maris; Jack T Pronk; Mark C M van Loosdrecht
Journal:  Appl Environ Microbiol       Date:  2018-08-31       Impact factor: 4.792

4.  Metabolic Interactions of a Chain Elongation Microbiome.

Authors:  Wenhao Han; Pinjing He; Liming Shao; Fan Lü
Journal:  Appl Environ Microbiol       Date:  2018-10-30       Impact factor: 4.792

5.  High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles.

Authors:  Michiel H In 't Zandt; Nardy Kip; Jeroen Frank; Stefan Jansen; Johannes A van Veen; Mike S M Jetten; Cornelia U Welte
Journal:  Appl Environ Microbiol       Date:  2019-10-01       Impact factor: 4.792

6.  MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies.

Authors:  Terry Ma; Di Xiao; Xin Xing
Journal:  Bioinformatics       Date:  2020-01-15       Impact factor: 6.937

7.  SolidBin: improving metagenome binning with semi-supervised normalized cut.

Authors:  Ziye Wang; Zhengyang Wang; Yang Young Lu; Fengzhu Sun; Shanfeng Zhu
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

8.  Asgard archaea illuminate the origin of eukaryotic cellular complexity.

Authors:  Katarzyna Zaremba-Niedzwiedzka; Eva F Caceres; Jimmy H Saw; Disa Bäckström; Lina Juzokaite; Emmelien Vancaester; Kiley W Seitz; Karthik Anantharaman; Piotr Starnawski; Kasper U Kjeldsen; Matthew B Stott; Takuro Nunoura; Jillian F Banfield; Andreas Schramm; Brett J Baker; Anja Spang; Thijs J G Ettema
Journal:  Nature       Date:  2017-01-11       Impact factor: 49.962

9.  Improved metagenome binning and assembly using deep variational autoencoders.

Authors:  Jakob Nybo Nissen; Joachim Johansen; Rosa Lundbye Allesøe; Casper Kaae Sønderby; Jose Juan Almagro Armenteros; Christopher Heje Grønbech; Lars Juhl Jensen; Henrik Bjørn Nielsen; Thomas Nordahl Petersen; Ole Winther; Simon Rasmussen
Journal:  Nat Biotechnol       Date:  2021-01-04       Impact factor: 54.908

Review 10.  Toward Accurate and Quantitative Comparative Metagenomics.

Authors:  Stephen Nayfach; Katherine S Pollard
Journal:  Cell       Date:  2016-08-25       Impact factor: 41.582
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.