Literature DB >> 20959381

SmashCommunity: a metagenomic annotation and analysis tool.

Manimozhiyan Arumugam1, Eoghan D Harrington, Konrad U Foerstner, Jeroen Raes, Peer Bork.   

Abstract

SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. AVAILABILITY: SmashCommunity source code and documentation are available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Entities:  

Mesh：

Year:  2010        PMID： 20959381     DOI： 10.1093/bioinformatics/btq536

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  44 in total

1.  Accurate and universal delineation of prokaryotic species.

Authors:  Daniel R Mende; Shinichi Sunagawa; Georg Zeller; Peer Bork
Journal:  Nat Methods       Date:  2013-07-28       Impact factor: 28.547

Review 2.  A clinician's guide to microbiome analysis.

Authors:  Marcus J Claesson; Adam G Clooney; Paul W O'Toole
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2017-08-09       Impact factor: 46.802

3.  Human gut microbes impact host serum metabolome and insulin sensitivity.

Authors:  Helle Krogh Pedersen; Valborg Gudmundsdottir; Henrik Bjørn Nielsen; Tuulia Hyotylainen; Trine Nielsen; Benjamin A H Jensen; Kristoffer Forslund; Falk Hildebrand; Edi Prifti; Gwen Falony; Emmanuelle Le Chatelier; Florence Levenez; Joel Doré; Ismo Mattila; Damian R Plichta; Päivi Pöhö; Lars I Hellgren; Manimozhiyan Arumugam; Shinichi Sunagawa; Sara Vieira-Silva; Torben Jørgensen; Jacob Bak Holm; Kajetan Trošt; Karsten Kristiansen; Susanne Brix; Jeroen Raes; Jun Wang; Torben Hansen; Peer Bork; Søren Brunak; Matej Oresic; S Dusko Ehrlich; Oluf Pedersen
Journal:  Nature       Date:  2016-07-13       Impact factor: 49.962

4.  Classification and quantification of bacteriophage taxa in human gut metagenomes.

Authors:  Alison S Waller; Takuji Yamada; David M Kristensen; Jens Roat Kultima; Shinichi Sunagawa; Eugene V Koonin; Peer Bork
Journal:  ISME J       Date:  2014-03-13       Impact factor: 10.302

Review 5.  The role of the intestinal microbiota in type 1 diabetes mellitus.

Authors:  Mikael Knip; Heli Siljander
Journal:  Nat Rev Endocrinol       Date:  2016-01-04       Impact factor: 43.330

6.  Enterotypes of the human gut microbiome.

Authors:  Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R Mende; Gabriel R Fernandes; Julien Tap; Thomas Bruls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; Francesc Casellas; Leyden Fernandez; Laurent Gautier; Torben Hansen; Masahira Hattori; Tetsuya Hayashi; Michiel Kleerebezem; Ken Kurokawa; Marion Leclerc; Florence Levenez; Chaysavanh Manichanh; H Bjørn Nielsen; Trine Nielsen; Nicolas Pons; Julie Poulain; Junjie Qin; Thomas Sicheritz-Ponten; Sebastian Tims; David Torrents; Edgardo Ugarte; Erwin G Zoetendal; Jun Wang; Francisco Guarner; Oluf Pedersen; Willem M de Vos; Søren Brunak; Joel Doré; María Antolín; François Artiguenave; Hervé M Blottiere; Mathieu Almeida; Christian Brechot; Carlos Cara; Christian Chervaux; Antonella Cultrone; Christine Delorme; Gérard Denariaz; Rozenn Dervyn; Konrad U Foerstner; Carsten Friss; Maarten van de Guchte; Eric Guedon; Florence Haimet; Wolfgang Huber; Johan van Hylckama-Vlieg; Alexandre Jamet; Catherine Juste; Ghalia Kaci; Jan Knol; Omar Lakhdari; Severine Layec; Karine Le Roux; Emmanuelle Maguin; Alexandre Mérieux; Raquel Melo Minardi; Christine M'rini; Jean Muller; Raish Oozeer; Julian Parkhill; Pierre Renault; Maria Rescigno; Nicolas Sanchez; Shinichi Sunagawa; Antonio Torrejon; Keith Turner; Gaetana Vandemeulebrouck; Encarna Varela; Yohanan Winogradsky; Georg Zeller; Jean Weissenbach; S Dusko Ehrlich; Peer Bork
Journal:  Nature       Date:  2011-04-20       Impact factor: 49.962

7.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Authors:  Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop
Journal:  Genome Biol       Date:  2013-01-15       Impact factor: 13.583

8.  SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Authors:  Eoghan D Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David A Relman
Journal:  Bioinformatics       Date:  2010-10-21       Impact factor: 6.937

9.  An integrated catalog of reference genes in the human gut microbiome.

Authors:  Junhua Li; Huijue Jia; Xianghang Cai; Huanzi Zhong; Qiang Feng; Shinichi Sunagawa; Manimozhiyan Arumugam; Jens Roat Kultima; Edi Prifti; Trine Nielsen; Agnieszka Sierakowska Juncker; Chaysavanh Manichanh; Bing Chen; Wenwei Zhang; Florence Levenez; Juan Wang; Xun Xu; Liang Xiao; Suisha Liang; Dongya Zhang; Zhaoxi Zhang; Weineng Chen; Hailong Zhao; Jumana Yousuf Al-Aama; Sherif Edris; Huanming Yang; Jian Wang; Torben Hansen; Henrik Bjørn Nielsen; Søren Brunak; Karsten Kristiansen; Francisco Guarner; Oluf Pedersen; Joel Doré; S Dusko Ehrlich; Peer Bork; Jun Wang
Journal:  Nat Biotechnol       Date:  2014-07-06       Impact factor: 54.908

Review 10.  High-resolution characterization of the human microbiome.

Authors:  Cecilia Noecker; Colin P McNally; Alexander Eng; Elhanan Borenstein
Journal:  Transl Res       Date:  2016-07-25       Impact factor: 7.012
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