From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

Critical Assessment of Metagenome Interpretation: the second round of challenges

(2022) Fernando Meyer et al.   NATURE METHODS

TIPP2: metagenomic taxonomic profiling using phylogenetic markers

(2021) Nidhi Shah et al.   BIOINFORMATICS

Challenges in benchmarking metagenomic profilers

(2021) Zheng Sun et al.   NATURE METHODS

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

(2021) Donovan H. Parks et al.   Frontiers in Microbiology

A standardized archaeal taxonomy for the Genome Taxonomy Database

(2021) Christian Rinke et al.   Nature Microbiology

The use of taxon-specific reference databases compromises metagenomic classification

(2020) Vanessa R. Marcelino et al.   BMC GENOMICS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

(2019) D B Dhakan et al.   GigaScience

Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels

(2019) Ana Lokmer et al.   PLoS One

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Metagenomic Functional Shifts to Plant Induced Environmental Changes

(2019) Svetlana N. Yurgel et al.   Frontiers in Microbiology

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

(2019) Javier Tamames et al.   BMC GENOMICS

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

(2018) Katherine R. Amato et al.   ISME Journal

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

(2018) Aaron M. Walsh et al.   Microbiome

Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics

(2018) Alejandra Escobar-Zepeda et al.   Scientific Reports

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals

(2017) Emma C. L. Finlayson-Trick et al.   PLoS One

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Higher classification sensitivity of short metagenomic reads with CLARK- S

(2016) Rachid Ounit et al.   BIOINFORMATICS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico

(2015) Lauren E. Gillies et al.   ENVIRONMENTAL MICROBIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

(2014) Nur A. Hasan et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

A framework for human microbiome research

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH