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MOCAT2: a metagenomic assembly, annotation and profiling framework

Jens Roat Kultima, Luis Pedro Coelho, Kristoffer Forslund, Jaime Huerta-Cepas, Simone S. Li, Marja Driessen, Anita Yvonne Voigt, Georg Zeller, Shinichi Sunagawa, Peer Bork
2016 Bioinformatics  
MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling.  ...  The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and  ...  Acknowledgements We wish to thank Bernd Klaus for valuable feedback on statistical analyses and Alison Waller for kindly providing the prophages database. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btw183 pmid:27153620 pmcid:PMC4978931 fatcat:njanfdmrb5fy7ocmj5x56i4yby

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes
2021 Microbiome  
We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data.  ...  At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.  ...  Acknowledgements We are grateful for the feedback and beta-testing by Susana Martinez Arbas.  ... 
doi:10.1186/s40168-020-00993-9 pmid:33597026 fatcat:6vlejnqtdbffbiktbyn45yvlk4

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
2019 Microbiome  
Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community.  ...  Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline.  ...  Beta users of NGLess are thanked for their feedback and bug reports.  ... 
doi:10.1186/s40168-019-0684-8 pmid:31159881 pmcid:PMC6547473 fatcat:a44vlibljvebhl2gs7vwfllbnq

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language [article]

Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
2018 bioRxiv   pre-print
Using this framework, we developed 'NG-meta-profiler', a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling  ...  It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible.  ...  Beta users of NGLess are thanked for their feedback and bug reports.  ... 
doi:10.1101/367755 fatcat:g6tzdy2y6zfhpeqb5dsxsfgcia

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
2017 Molecular biology and evolution  
We, therefore, developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database  ...  Finally, we evaluated eggNOG-mapper for functional annotation of metagenomics data, yielding better performance than interProScan. eggNOG-mapper runs $15Â faster than BLAST and at least 2.5Â faster than  ...  Acknowledgements The research leading to these results has received funding from: The European Union Seventh Framework Programme (FP7/2007(FP7/ -2013  ... 
doi:10.1093/molbev/msx148 pmid:28460117 pmcid:PMC5850834 fatcat:dvdoactxljd6ldc73vantqinf4

Metagenomic tools in microbial ecology research

Neslihan Taş, Anniek Ee de Jong, Yaoming Li, Gareth Trubl, Yaxin Xue, Nicholas C Dove
2021 Current Opinion in Biotechnology  
While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous  ...  Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding  ...  Acknowledgements Funding for this work was provided to Neslihan Taş The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States  ... 
doi:10.1016/j.copbio.2021.01.019 pmid:33592536 fatcat:bjbwezen7zghnmew55gb6ux2d4

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview

Partho Sen, Matej Orešič
2019 Metabolites  
Taxonomic and functional profiling of the gut microbiome by next-generation sequencing (NGS) has unveiled substantial richness and diversity.  ...  Furthermore, we summarize various tools and resources available for metagenomic data processing and GSMM, highlighting the experimental approaches needed to validate the model predictions.  ...  Acknowledgments: We thank to Alex Dickens and Santosh Lamichhane for helpful scientific discussions. We also  ... 
doi:10.3390/metabo9020022 pmid:30695998 pmcid:PMC6410263 fatcat:3xgsy2jrxfe2ld4uhubvpfrefa

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples [article]

Carlos S. Casimiro-Soriguer, Carlos Loucera, Javier Perez Florido, Daniel López-López, Joaquin Dopazo
2018 bioRxiv   pre-print
that account for bacterial metabolism and other cell functionalities.  ...  Typical microbiome studies involve the analysis of bacterial abundance profiles.ResultsHere we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles  ...  MOCAT2 pre-computed eggNOG orthologous groups sequences with annotations from other databases.  ... 
doi:10.1101/476853 fatcat:5g6uyknb5bgkpkwrtj2wybfnve

A review of methods and databases for metagenomic classification and assembly

Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg
2017 Briefings in Bioinformatics  
His laboratory conducts research on DNA and RNA sequence analysis including genome assembly, transcriptome assembly, sequence alignment and metagenomics.  ...  Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods.  ...  MOCAT2 [109] integrates read filtering, taxonomic profiling with mOTU [82] , assembly, gene prediction and annotation to output taxonomic as well as functional profiles of metagenomics samples.  ... 
doi:10.1093/bib/bbx120 pmid:29028872 fatcat:lpy4gbxtyzdb5jyz7bh2zdz7iq

Conducting metagenomic studies in microbiology and clinical research

Tiphaine C. Martin, Alessia Visconti, Tim D. Spector, Mario Falchi
2018 Applied Microbiology and Biotechnology  
Here, we present an overview of the challenges and opportunities involved in conducting a metagenomic study, with a particular focus on data processing and analytical methods.  ...  Owing to the increased cost-effectiveness of high-throughput technologies, the number of studies focusing on the human microbiome and its connections to human health and disease has recently surged.  ...  AV would like to thank Brian Bushnell for his helpful suggestions about how to use the BBTools suite in a metagenomics context and for providing several useful resources.  ... 
doi:10.1007/s00253-018-9209-9 pmid:30078138 fatcat:zd4kwgmo6nhihicpe3bcpp7kme

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Ana Elena Pérez-Cobas, Laura Gomez-Valero, Carmen Buchrieser
2020 Microbial Genomics  
Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge.  ...  Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples.  ...  Functional annotation and taxonomic profiling Functional annotation of WGS metagenomics allows one to answer the question, which functional capacities are encoded in a microbial community?  ... 
doi:10.1099/mgen.0.000409 pmid:32706331 fatcat:lv23zgejzzf45pmetzsb52kdlm

An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome

Rohan M. Shah, Elizabeth J. McKenzie, Magda T. Rosin, Snehal R. Jadhav, Shakuntla V. Gondalia, Douglas Rosendale, David J. Beale
2020 Metabolites  
Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related  ...  In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford.  ...  Acknowledgments: The authors would like to acknowledge and thank the contributions and comments of Starin McKeen, Caterina Carco and Shanalee James during the preparation of this manuscript.  ... 
doi:10.3390/metabo10030094 pmid:32155792 pmcid:PMC7143645 fatcat:zyn3vvzg5zahzbo7c5ggzzbzn4

ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data

Theodoros Koutsandreas, Efthymios Ladoukakis, Eleftherios Pilalis, Dimitra Zarafeta, Fragiskos N. Kolisis, Georgios Skretas, Aristotelis A. Chatziioannou
2019 Frontiers in Genetics  
ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to  ...  At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation.  ...  Anders Krogh, from University of Copenhagen for providing access to their university server in order to conduct a series of tests for our numerous bioinformatic tools and platforms and install our beta  ... 
doi:10.3389/fgene.2019.00469 pmid:31178894 pmcid:PMC6543708 fatcat:5b22zyjjhfcxjpojwmw4szedtu

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

Alejandra Escobar-Zepeda, Arturo Vera-Ponce de León, Alejandro Sanchez-Flores
2015 Frontiers in Genetics  
in a metagenome.  ...  New computational methods are constantly developed to collect, process, and extract useful biological information from a variety of samples and complex datasets, but metagenomics needs the integration  ...  ACKNOWLEDGMENTS AE and AV are Ph.D. students from Programa de Doctorado en Ciencias Bioquímicas and Programa de Doctorado en Ciencias Biomédicas Universidad Nacional Autónoma de México (UNAM) with scholarship  ... 
doi:10.3389/fgene.2015.00348 pmid:26734060 pmcid:PMC4681832 fatcat:2f7f7fybdnhtnddsyawd4qjsbm

A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities

Qi Li, Feibi Lin, Chen Yang, Juanping Wang, Yan Lin, Mengyuan Shen, Min S. Park, Tao Li, Jindong Zhao
2018 Frontiers in Microbiology  
Our integrated metagenomic pipeline consisted of efficient assembly, binning, annotation, and quality assurance methods that ensured high-quality genome reconstruction.  ...  We conducted a comprehensive metagenomic study that analyzed species diversity, community structure, functional components, metabolic pathways and networks to investigate functional interactions among  ...  Construction of a Microcystis Microbiome Reference Genome Catalog The integrated metagenomic pipeline, which consisted of efficient assembly, binning, annotation, and quality assurance methods, facilitated  ... 
doi:10.3389/fmicb.2018.00746 pmid:29731741 pmcid:PMC5919953 fatcat:jxyzx4yvkvewpbhvirf4i3azte
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