Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
Authors
Keywords
-
Journal
Nature Protocols
Volume 16, Issue 5, Pages 2520-2541
Publisher
Springer Science and Business Media LLC
Online
2021-04-17
DOI
10.1038/s41596-021-00508-2
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
- (2021) Matthew R. Olm et al. NATURE BIOTECHNOLOGY
- Accurate and complete genomes from metagenomes
- (2020) Lin-Xing Chen et al. GENOME RESEARCH
- A complete domain-to-species taxonomy for Bacteria and Archaea
- (2020) Donovan H. Parks et al. NATURE BIOTECHNOLOGY
- Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing
- (2020) Hui-yu Sui et al. Frontiers in Microbiology
- To Dereplicate or Not To Dereplicate?
- (2020) Jacob T. Evans et al. mSphere
- A unified catalog of 204,938 reference genomes from the human gut microbiome
- (2020) Alexandre Almeida et al. NATURE BIOTECHNOLOGY
- Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands
- (2020) Finlay Maguire et al. Microbial Genomics
- 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
- A human gut bacterial genome and culture collection for improved metagenomic analyses
- (2019) Samuel C. Forster et al. NATURE BIOTECHNOLOGY
- Novel insights from uncultivated genomes of the global human gut microbiome
- (2019) Stephen Nayfach et al. NATURE
- A new genomic blueprint of the human gut microbiota
- (2019) Alexandre Almeida et al. NATURE
- Workflow systems turn raw data into scientific knowledge
- (2019) Jeffrey M. Perkel NATURE
- Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
- (2019) Taylor M. Royalty et al. mSystems
- GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
- (2019) Pierre-Alain Chaumeil et al. BIOINFORMATICS
- Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
- (2018) Robert D. Stewart et al. Nature Communications
- Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
- (2018) Christian M. K. Sieber et al. Nature Microbiology
- Genome-centric view of carbon processing in thawing permafrost
- (2018) Ben J. Woodcroft et al. NATURE
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
- (2018) Gherman V. Uritskiy et al. Microbiome
- Identification and removal of contaminating microbial DNA from PCR reagents: impact on low‐biomass microbiome analyses
- (2018) L.F. Stinson et al. LETTERS IN APPLIED MICROBIOLOGY
- Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
- (2018) Lindsey M. Solden et al. Nature Microbiology
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
- Performing Skin Microbiome Research: A Method to the Madness
- (2017) Heidi H. Kong et al. JOURNAL OF INVESTIGATIVE DERMATOLOGY
- Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- (2017) Robert M Bowers et al. NATURE BIOTECHNOLOGY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
- (2017) John Vollmers et al. PLoS One
- Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
- (2017) Donovan H. Parks et al. Nature Microbiology
- Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
- (2017) Karel Sedlar et al. Computational and Structural Biotechnology Journal
- Temporal Stability of the Human Skin Microbiome
- (2016) Julia Oh et al. CELL
- Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
- (2016) Karthik Anantharaman et al. Nature Communications
- Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
- (2016) Hsin-Hung Lin et al. Scientific Reports
- Reconstructing 16S rRNA genes in metagenomic data
- (2015) Cheng Yuan et al. BIOINFORMATICS
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Complete nitrification by a single microorganism
- (2015) Maartje A. H. J. van Kessel et al. NATURE
- Complete nitrification by Nitrospira bacteria
- (2015) Holger Daims et al. NATURE
- Assembly: a resource for assembled genomes at NCBI
- (2015) Paul A. Kitts et al. NUCLEIC ACIDS RESEARCH
- Microbial species delineation using whole genome sequences
- (2015) Neha J. Varghese et al. NUCLEIC ACIDS RESEARCH
- GenBank
- (2015) Karen Clark et al. NUCLEIC ACIDS RESEARCH
- Library preparation methodology can influence genomic and functional predictions in human microbiome research
- (2015) Marcus B. Jones et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Anvi’o: an advanced analysis and visualization platform for ‘omics data
- (2015) A. Murat Eren et al. PeerJ
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- A first look at the Oxford Nanopore MinION sequencer
- (2014) Alexander S. Mikheyev et al. Molecular Ecology Resources
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways
- (2014) R. Cameron Coates et al. PLoS One
- Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
- (2013) M. S. Fitzsimons et al. GENOME RESEARCH
- Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant
- (2013) Nest McKain et al. JOURNAL OF MICROBIOLOGICAL METHODS
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology
- (2010) Alice McCarthy CHEMISTRY & BIOLOGY
- Comparison of 61 Sequenced Escherichia coli Genomes
- (2010) Oksana Lukjancenko et al. MICROBIAL ECOLOGY
- Unsupervised statistical clustering of environmental shotgun sequences
- (2009) Andrey Kislyuk et al. BMC BIOINFORMATICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More