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Literature DB >> 23320958

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

Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop.

Abstract

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2013 PMID： 23320958 PMCID： PMC4053804 DOI： 10.1186/gb-2013-14-1-r2

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

72 in total

1. Individual genome assembly from complex community short-read metagenomic datasets.

Authors: Chengwei Luo; Despina Tsementzi; Nikos C Kyrpides; Konstantinos T Konstantinidis
Journal: ISME J Date: 2011-10-27 Impact factor: 10.302

2. GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Authors: Steven L Salzberg; Adam M Phillippy; Aleksey Zimin; Daniela Puiu; Tanja Magoc; Sergey Koren; Todd J Treangen; Michael C Schatz; Arthur L Delcher; Michael Roberts; Guillaume Marçais; Mihai Pop; James A Yorke
Journal: Genome Res Date: 2012-01-06 Impact factor: 9.043

3. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors: Daniel R Zerbino; Ewan Birney
Journal: Genome Res Date: 2008-03-18 Impact factor: 9.043

4. Prokaryotic gene prediction using GeneMark and GeneMark.hmm.

Authors: Mark Borodovsky; Ryan Mills; John Besemer; Alex Lomsadze
Journal: Curr Protoc Bioinformatics Date: 2003-05

5. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

Authors: F Meyer; D Paarmann; M D'Souza; R Olson; E M Glass; M Kubal; T Paczian; A Rodriguez; R Stevens; A Wilke; J Wilkening; R A Edwards
Journal: BMC Bioinformatics Date: 2008-09-19 Impact factor: 3.169

6. A core gut microbiome in obese and lean twins.

Authors: Peter J Turnbaugh; Micah Hamady; Tanya Yatsunenko; Brandi L Cantarel; Alexis Duncan; Ruth E Ley; Mitchell L Sogin; William J Jones; Bruce A Roe; Jason P Affourtit; Michael Egholm; Bernard Henrissat; Andrew C Heath; Rob Knight; Jeffrey I Gordon
Journal: Nature Date: 2008-11-30 Impact factor: 49.962

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

1. Individual genome assembly from complex community short-read metagenomic datasets.

2. GAGE: A critical evaluation of genome assemblies and assembly algorithms.

3. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

4. Prokaryotic gene prediction using GeneMark and GeneMark.hmm.

5. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

6. A core gut microbiome in obese and lean twins.

7. Aggressive assembly of pyrosequencing reads with mates.

8. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis.

9. Phylogenetic classification of short environmental DNA fragments.

10. Genome assembly forensics: finding the elusive mis-assembly.

1. TruSPAdes: barcode assembly of TruSeq synthetic long reads.

2. Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.

3. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.

4. Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer.

Review 5. Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research.

Review 6. A clinician's guide to microbiome analysis.

Review 7. Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics.

8. DIME: a novel framework for de novo metagenomic sequence assembly.

Review 9. A review of methods and databases for metagenomic classification and assembly.

Review 10. Enteric Virome and Carcinogenesis in the Gut.