Metagenomics ≈ Metagenomics
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VSEARCH: a versatile open source tool for metagenomics Open
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USE…
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads Open
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long re…
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Improved metagenomic analysis with Kraken 2 Open
Although Kraken’s k -mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by…
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Open
Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in p…
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metaSPAdes: a new versatile metagenomic assembler Open
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacter…
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Evolutionary-scale prediction of atomic-level protein structure with a language model Open
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a …
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Open
Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional…
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PHASTER: a better, faster version of the PHAST phage search tool Open
PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phag…
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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Open
We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular…
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Mash: fast genome and metagenome distance estimation using MinHash Open
Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences a…
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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data Open
Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles…
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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Open
Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available throug…
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Microbiome Datasets Are Compositional: And This Is Not Optional Open
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environm…
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dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication Open
The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively …
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BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics Open
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented…
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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation Open
Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for …
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Bracken: estimating species abundance in metagenomics data Open
Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of …
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Open
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to acc…
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns Open
Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose am…
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MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics Open
Thanks to the development of high‐throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. …
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MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data Open
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex…
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The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota Open
SUMMARY The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of…
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MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data Open
There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples…
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Clinical metagenomics Open
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging appro…
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VFDB 2022: a general classification scheme for bacterial virulence factors Open
The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologi…
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Centrifuge: rapid and sensitive classification of metagenomic sequences Open
Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transfo…
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Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection Open
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its a…
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Human gut microbiome: hopes, threats and promises Open
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention b…
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HH-suite3 for fast remote homology detection and deep protein annotation Open
Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple seq…
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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Open
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such envi…