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

Genome Biology
Todd J TreangenMihai 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.

Citations

Sep 24, 2013·Bioinformatics·Jurgen F NijkampDick de Ridder
Feb 26, 2014·BMC Genomics·Satish M Srinivasan, Chittibabu Guda
Oct 23, 2013·PLoS Computational Biology·Rogan CarrElhanan Borenstein
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
Jun 3, 2014·BMC Bioinformatics·Sergey KorenAdam M Phillippy
Jun 21, 2014·Bioinformatics·Bahlul HaiderChongle Pan
Aug 12, 2014·Systematic Biology·Frederick A Matsen
Feb 2, 2016·Nature Methods·Anton Bankevich, Pavel A Pevzner
Dec 15, 2015·Nature Biotechnology·Volodymyr KuleshovMichael Snyder
Nov 26, 2015·Fertility and Sterility·Amir MorJames H Segars
Apr 12, 2016·Frontiers in Microbiology·Jonathan VerneauPhilippe Colson
Dec 15, 2015·Biotechnology Research International·Satish KumarManoj Pandit Brahmane
Jul 26, 2015·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Fiona ThorburnPablo R Murcia
Aug 27, 2015·Microbiome·Emily B HollisterJames Versalovic
Apr 29, 2015·Biotechnology Advances·M Sofía UrbietaKian Mau Goh
Aug 8, 2015·BMC Bioinformatics·Binbin LaiHuaiqiu Zhu
Jun 15, 2015·Bioinformatics·Cheng YuanYanni Sun
May 6, 2016·Frontiers in Microbiology·Juan JovelGane K-S Wong
Oct 4, 2014·Frontiers in Microbiology·Alinne P de CastroOctávio L Franco
Dec 6, 2014·Frontiers in Cell and Developmental Biology·Efthymios LadoukakisAristotelis A Chatziioannou
Jul 2, 2014·Frontiers in Plant Science·Thomas J Sharpton
Feb 17, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xuan GuoYi Pan
Jan 8, 2015·Advances in Wound Care·Brendan P Hodkinson, Elizabeth A Grice
Nov 26, 2015·PLoS Computational Biology·Mikhail ShugayDmitriy M Chudakov
Jun 5, 2016·Bioinformatics·Vladimir I UlyantsevDmitry G Alexeev
Nov 2, 2016·Environmental Science & Technology·Joao GaticaEddie Cytryn
Mar 23, 2017·Frontiers in Genetics·Despoina D RoumpekaMick Watson
Mar 17, 2017·Genome Research·Sergey NurkPavel A Pevzner
Apr 6, 2017·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Michel DrancourtDidier Raoult
Dec 23, 2016·Médecine sciences : M/S·Patrick VeigaMuriel Derrien
Nov 11, 2017·Frontiers in Microbiology·Serajus SalaheenDebabrata Biswas
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRS077736

Software Mentioned

Arachne
MetaPhyler
CABOG
AMOS
HUMAnN
MetaHit
Perl
SC
Ruffus
PHMMER

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.