Literature DB >> 29917068

YAMP: a containerized workflow enabling reproducibility in metagenomics research.

Alessia Visconti1, Tiphaine C Martin1, Mario Falchi1.   

Abstract

YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.

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Year:  2018        PMID： 29917068      PMCID： PMC6047416          DOI： 10.1093/gigascience/giy072

Source DB:  PubMed          Journal:  Gigascience        ISSN： 2047-217X            Impact factor:   6.524


  51 in total

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Journal:  Science       Date:  2011-12-02       Impact factor: 47.728

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Journal:  Nat Genet       Date:  2008-01-28       Impact factor: 38.330

3.  Systematic artifacts in metagenomes from complex microbial communities.

Authors:  Vicente Gomez-Alvarez; Tracy K Teal; Thomas M Schmidt
Journal:  ISME J       Date:  2009-07-09       Impact factor: 10.302

4.  Nextflow enables reproducible computational workflows.

Authors:  Paolo Di Tommaso; Maria Chatzou; Evan W Floden; Pablo Prieto Barja; Emilio Palumbo; Cedric Notredame
Journal:  Nat Biotechnol       Date:  2017-04-11       Impact factor: 54.908

5.  Metabolic reconstruction for metagenomic data and its application to the human microbiome.

Authors:  Sahar Abubucker; Nicola Segata; Johannes Goll; Alyxandria M Schubert; Jacques Izard; Brandi L Cantarel; Beltran Rodriguez-Mueller; Jeremy Zucker; Mathangi Thiagarajan; Bernard Henrissat; Owen White; Scott T Kelley; Barbara Methé; Patrick D Schloss; Dirk Gevers; Makedonka Mitreva; Curtis Huttenhower
Journal:  PLoS Comput Biol       Date:  2012-06-13       Impact factor: 4.475

6.  The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Authors:  Ross Overbeek; Tadhg Begley; Ralph M Butler; Jomuna V Choudhuri; Han-Yu Chuang; Matthew Cohoon; Valérie de Crécy-Lagard; Naryttza Diaz; Terry Disz; Robert Edwards; Michael Fonstein; Ed D Frank; Svetlana Gerdes; Elizabeth M Glass; Alexander Goesmann; Andrew Hanson; Dirk Iwata-Reuyl; Roy Jensen; Neema Jamshidi; Lutz Krause; Michael Kubal; Niels Larsen; Burkhard Linke; Alice C McHardy; Folker Meyer; Heiko Neuweger; Gary Olsen; Robert Olson; Andrei Osterman; Vasiliy Portnoy; Gordon D Pusch; Dmitry A Rodionov; Christian Rückert; Jason Steiner; Rick Stevens; Ines Thiele; Olga Vassieva; Yuzhen Ye; Olga Zagnitko; Veronika Vonstein
Journal:  Nucleic Acids Res       Date:  2005-10-07       Impact factor: 16.971

7.  Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

Authors:  Daniel Garijo; Sarah Kinnings; Li Xie; Lei Xie; Yinliang Zhang; Philip E Bourne; Yolanda Gil
Journal:  PLoS One       Date:  2013-11-27       Impact factor: 3.240

Review 8.  Integrative workflows for metagenomic analysis.

Authors:  Efthymios Ladoukakis; Fragiskos N Kolisis; Aristotelis A Chatziioannou
Journal:  Front Cell Dev Biol       Date:  2014-11-19

Review 9.  Tools and techniques for computational reproducibility.

Authors:  Stephen R Piccolo; Michael B Frampton
Journal:  Gigascience       Date:  2016-07-11       Impact factor: 6.524

10.  EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

Authors:  Alex L Mitchell; Maxim Scheremetjew; Hubert Denise; Simon Potter; Aleksandra Tarkowska; Matloob Qureshi; Gustavo A Salazar; Sebastien Pesseat; Miguel A Boland; Fiona M I Hunter; Petra Ten Hoopen; Blaise Alako; Clara Amid; Darren J Wilkinson; Thomas P Curtis; Guy Cochrane; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971
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  5 in total

1.  YAMP: a containerized workflow enabling reproducibility in metagenomics research.

Authors:  Alessia Visconti; Tiphaine C Martin; Mario Falchi
Journal:  Gigascience       Date:  2018-07-01       Impact factor: 6.524

2.  Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.

Authors:  Casper S Poulsen; Claus T Ekstrøm; Frank M Aarestrup; Sünje J Pamp
Journal:  Microbiol Spectr       Date:  2022-03-15

Review 3.  Conducting metagenomic studies in microbiology and clinical research.

Authors:  Tiphaine C Martin; Alessia Visconti; Tim D Spector; Mario Falchi
Journal:  Appl Microbiol Biotechnol       Date:  2018-08-04       Impact factor: 4.813

4.  Interplay between the human gut microbiome and host metabolism.

Authors:  Alessia Visconti; Caroline I Le Roy; Fabio Rosa; Niccolò Rossi; Tiphaine C Martin; Robert P Mohney; Weizhong Li; Emanuele de Rinaldis; Jordana T Bell; J Craig Venter; Karen E Nelson; Tim D Spector; Mario Falchi
Journal:  Nat Commun       Date:  2019-10-03       Impact factor: 14.919

5.  MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline.

Authors:  Alexander Eng; Adrian J Verster; Elhanan Borenstein
Journal:  BMC Bioinformatics       Date:  2020-10-21       Impact factor: 3.169
  5 in total

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