Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Authors
Keywords
-
Journal
Nature Protocols
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-03-02
DOI
10.1038/s41596-020-00480-3
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- DeepMAsED: Evaluating the quality of metagenomic assemblies
- (2020) Olga Mineeva et al. BIOINFORMATICS
- Complete, closed bacterial genomes from microbiomes using nanopore sequencing
- (2020) Eli L. Moss et al. NATURE BIOTECHNOLOGY
- A unified catalog of 204,938 reference genomes from the human gut microbiome
- (2020) Alexandre Almeida et al. NATURE BIOTECHNOLOGY
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
- (2019) Edoardo Pasolli et al. CELL
- CAMISIM: simulating metagenomes and microbial communities
- (2019) Adrian Fritz et al. Microbiome
- Systematic benchmarking of omics computational tools
- (2019) Serghei Mangul et al. Nature Communications
- Microbial abundance, activity and population genomic profiling with mOTUs2
- (2019) Alessio Milanese et al. Nature Communications
- A new genomic blueprint of the human gut microbiota
- (2019) Alexandre Almeida et al. NATURE
- Long-Read Sequencing Emerging in Medical Genetics
- (2019) Tuomo Mantere et al. Frontiers in Genetics
- Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation
- (2019) Gaia Andreoletti et al. HUMAN MUTATION
- Benchmarking Metagenomics Tools for Taxonomic Classification
- (2019) Simon H. Ye et al. CELL
- Bioconda: sustainable and comprehensive software distribution for the life sciences
- (2018) Björn Grüning et al. NATURE METHODS
- AMBER: Assessment of Metagenome BinnERs
- (2018) Fernando Meyer et al. GigaScience
- Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
- (2018) Christian M. K. Sieber et al. Nature Microbiology
- Critical Assessment of Metagenome Interpretation Enters the Second Round
- (2018) Andreas Bremges et al. mSystems
- On the Road to Strain-Resolved Comparative Metagenomics
- (2018) Nicola Segata mSystems
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- Microbial strain-level population structure and genetic diversity from metagenomes
- (2017) Duy Tin Truong et al. GENOME RESEARCH
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- Nextflow enables reproducible computational workflows
- (2017) Paolo Di Tommaso et al. NATURE BIOTECHNOLOGY
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
- (2017) Alex L Mitchell et al. NUCLEIC ACIDS RESEARCH
- Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
- (2017) Donovan H. Parks et al. Nature Microbiology
- MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
- (2016) Dinghua Li et al. METHODS
- MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
- (2016) Daniel H. Huson et al. PLoS Computational Biology
- PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
- (2016) Ivan Gregor et al. PeerJ
- Next generation sequencing data of a defined microbial mock community
- (2016) Esther Singer et al. Scientific Data
- The FAIR Guiding Principles for scientific data management and stewardship
- (2016) Mark D. Wilkinson et al. Scientific Data
- An evaluation of the accuracy and speed of metagenome analysis tools
- (2016) Stinus Lindgreen et al. Scientific Reports
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- MetaQUAST: evaluation of metagenome assemblies
- (2015) Alla Mikheenko et al. BIOINFORMATICS
- SuRankCo: supervised ranking of contigs in de novo assemblies
- (2015) Mathias Kuhring et al. BMC BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Bioboxes: standardised containers for interchangeable bioinformatics software
- (2015) Peter Belmann et al. GigaScience
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
- (2013) Scott C. Clark et al. BIOINFORMATICS
- CAFA and the Open World of protein function predictions
- (2013) Christophe Dessimoz et al. TRENDS IN GENETICS
- Snakemake--a scalable bioinformatics workflow engine
- (2012) J. Koster et al. BIOINFORMATICS
- The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
- (2012) Daniel McDonald et al. GigaScience
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started