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MOCAT2: a metagenomic assembly, annotation and profiling framework

https://doi.org/10.1093/bioinformatics/btw183

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

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Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

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Classification and quantification of bacteriophage taxa in human gut metagenomes

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Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice

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Computational meta'omics for microbial community studies

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A human gut microbial gene catalogue established by metagenomic sequencing

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Biogeography and individuality shape function in the human skin metagenome

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An integrated catalog of reference genes in the human gut microbiome

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A catalog of the mouse gut metagenome

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Accurate and universal delineation of prokaryotic species

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Metagenomic species profiling using universal phylogenetic marker genes

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Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1093/bioinformatics/btq003openalex-snapshot

CD-HIT Suite: a web server for clustering and comparing biological sequences

inferredcites →https://doi.org/10.1093/bioinformatics/bts599openalex-snapshot

Real Time Metagenomics: Using k-mers to annotate metagenomes

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Curation, integration and visualization of bacterial virulence factors in PATRIC

inferredcites →https://doi.org/10.1093/bioinformatics/btu843openalex-snapshot

UProC: tools for ultra-fast protein domain classification

inferredcites →https://doi.org/10.1093/bioinformatics/btv584openalex-snapshot

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

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MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

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IMG/M: a data management and analysis system for metagenomes

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ARDB--Antibiotic Resistance Genes Database

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DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

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Strict control of transgene expression in a mouse model for sensitive biological applications based on RMCE compatible ES cells

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CoMet—a web server for comparative functional profiling of metagenomes

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ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

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DBETH: A Database of Bacterial Exotoxins for Human

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VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

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dbCAN: a web resource for automated carbohydrate-active enzyme annotation

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Data, information, knowledge and principle: back to metabolism in KEGG

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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

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Pfam: the protein families database

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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

inferredcites →https://doi.org/10.1093/nar/gkv1164openalex-snapshot

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

inferredcites →https://doi.org/10.1101/gr.120618.111openalex-snapshot

Integrative analysis of environmental sequences using MEGAN4

inferredcites →https://doi.org/10.1101/pdb.emo140openalex-snapshot

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

inferredcites →https://doi.org/10.1101/pdb.prot5368openalex-snapshot

Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes

inferredcites →https://doi.org/10.1126/science.1261359openalex-snapshot

Structure and function of the global ocean microbiome

inferredcites →https://doi.org/10.1128/aac.00419-13openalex-snapshot

The Comprehensive Antibiotic Resistance Database

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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

inferredcites →https://doi.org/10.1371/journal.pone.0041439openalex-snapshot

Atrophic Cardiac Remodeling Induced by Taurine Deficiency in Wistar Rats

inferredcites →https://doi.org/10.1371/journal.pone.0047656openalex-snapshot

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

inferredcites →https://doi.org/10.1371/journal.pone.0105067openalex-snapshot

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

inferredcites →https://doi.org/10.1371/journal.pone.0142102openalex-snapshot

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

inferredcites →https://doi.org/10.15252/msb.20145645openalex-snapshot

Potential of fecal microbiota for early‐stage detection of colorectal cancer

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Variation and transmission of the human gut microbiota across multiple familial generations

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Longitudinal multi-omics analyses of the gut–liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis

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Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires

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Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

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Unravelling the collateral damage of antibiotics on gut bacteria

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Combinatorial, additive and dose-dependent drug–microbiome associations

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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

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The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

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The maintenance of microbial community in human fecal samples by a cost effective preservation buffer

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Gut microbiota analysis in children with autism spectrum disorder and their family members

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Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

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Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli

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Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate

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Blood pressure changes correlate with short-chain fatty acid production potential shifts under a synbiotic intervention

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Novel sequencing technologies to support industrial biotechnology

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YAMP: a containerized workflow enabling reproducibility in metagenomics research

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

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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

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CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data

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Asymptomatic gut colonization by extended-spectrum beta-lactamase-producing Escherichia coli is not associated with an altered gut microbiome or metabolome in Dutch adults

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Distribution and survival strategies of diazotrophs in the Arctic Ocean revealed by global-scale metagenomic analysis

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Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

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The Gut Microbiome Strongly Mediates the impact of Lifestyle combined variables on Cardiometabolic Phenotypes

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YAMP: a containerised workflow enabling reproducibility in metagenomics research

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

inferred← citeshttps://doi.org/10.1101/375121openalex-snapshot

Carnelian: alignment-free functional binning and abundance estimation of metagenomic reads

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MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization

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Metagenome association study of the gut microbiome revealed biomarkers linked to chemotherapy outcomes in locally advanced and advanced lung cancer

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A primer on metagenomics and next‐generation sequencing in fish gut microbiome research

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Targeted protein evolution in the gut microbiome by diversity-generating retroelements

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Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

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Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost

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Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

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Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

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Fecal Microbiome Composition Does Not Predict Diet‐Induced TMAO Production in Healthy Adults

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High-throughput DNA sequencing technologies for water and wastewater analysis

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Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients

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Analysis and Interpretation of metagenomics data: an approach

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ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

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Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

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HirBin: high-resolution identification of differentially abundant functions in metagenomes

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A-GAME: improving the assembly of pooled functional metagenomics sequence data

inferred← citeshttps://doi.org/10.1186/s12866-020-02068-zopenalex-snapshot

Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study

inferred← citeshttps://doi.org/10.1186/s12916-022-02550-7openalex-snapshot

Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics

inferred← citeshttps://doi.org/10.1186/s12917-020-02732-6openalex-snapshot

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

inferred← citeshttps://doi.org/10.1186/s12920-024-01978-5openalex-snapshot

Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs

inferred← citeshttps://doi.org/10.1186/s13059-018-1540-zopenalex-snapshot

SKESA: strategic k-mer extension for scrupulous assemblies

inferred← citeshttps://doi.org/10.1186/s13059-020-1933-7openalex-snapshot

Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

inferred← citeshttps://doi.org/10.1186/s13059-021-02306-1openalex-snapshot

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

inferred← citeshttps://doi.org/10.1186/s13062-019-0246-9openalex-snapshot

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

inferred← citeshttps://doi.org/10.1186/s13068-020-01869-8openalex-snapshot

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

inferred← citeshttps://doi.org/10.1186/s13073-017-0428-yopenalex-snapshot

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

inferred← citeshttps://doi.org/10.1186/s13073-021-00840-yopenalex-snapshot

Guild-based analysis for understanding gut microbiome in human health and diseases

inferred← citeshttps://doi.org/10.1186/s13073-021-00869-zopenalex-snapshot

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home

inferred← citeshttps://doi.org/10.1186/s40168-018-0450-3openalex-snapshot

Similarity of the dog and human gut microbiomes in gene content and response to diet

inferred← citeshttps://doi.org/10.1186/s40168-018-0532-2openalex-snapshot

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

inferred← citeshttps://doi.org/10.1186/s40168-019-0684-8openalex-snapshot

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

inferred← citeshttps://doi.org/10.1186/s40168-019-0781-8openalex-snapshot

Metagenomic analysis reveals the microbiome and resistome in migratory birds

inferred← citeshttps://doi.org/10.1186/s40168-020-00993-9openalex-snapshot

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

inferred← citeshttps://doi.org/10.12688/f1000research.18866.1openalex-snapshot

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005252openalex-snapshot

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota

inferred← citeshttps://doi.org/10.15252/msb.20177589openalex-snapshot

Subspecies in the global human gut microbiome

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2237461/v1openalex-snapshot

Exploring Intervention of Selenium on Gut Microbiota Homeostasis and Corresponding Genetic Metabolism in Mice with Breast Cancer on a High-fat Diet Using Metagenomics Sequencing

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3433959/v1openalex-snapshot

Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3433959/v2openalex-snapshot

Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines

inferred← citeshttps://doi.org/10.21203/rs.3.rs-48380/v1openalex-snapshot

A metagenome association study of gut microbiome revealed biomarkers for chemotherapy efficacy in locally advanced and advanced lung cancer

inferred← citeshttps://doi.org/10.21303/2504-5695.2024.003336openalex-snapshot

Antimicrobial resistance as a global public health threat: the way forward

inferred← citeshttps://doi.org/10.2147/jir.s521991openalex-snapshot

Muscone Ameliorates High-Altitude Hypoxia Gastrointestinal Stress via Modulation of Lactobacillus Murinus and Mitochondrial Metabolism

inferred← citeshttps://doi.org/10.22541/au.159646791.16636826openalex-snapshot

Predominance of Extreme Environmental Conditions at High Altitude in Modulating Human Gut Microbiota

inferred← citeshttps://doi.org/10.26481/dis.20240417mdopenalex-snapshot

Colonisation of the gut microbiome by Escherichia coli during international travel

inferred← citeshttps://doi.org/10.2903/sp.efsa.2024.en-8602openalex-snapshot

Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

inferred← citeshttps://doi.org/10.33073/pjm-2025-006openalex-snapshot

Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals

inferred← citeshttps://doi.org/10.3389/fcimb.2019.00090openalex-snapshot

The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

inferred← citeshttps://doi.org/10.3389/fgene.2019.00469openalex-snapshot

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

inferred← citeshttps://doi.org/10.3389/fgene.2019.01344openalex-snapshot

Integrating Computational Methods to Investigate the Macroecology of Microbiomes

inferred← citeshttps://doi.org/10.3389/fmicb.2016.01521openalex-snapshot

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

inferred← citeshttps://doi.org/10.3389/fmicb.2018.00746openalex-snapshot

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

inferred← citeshttps://doi.org/10.3389/fmicb.2018.01451openalex-snapshot

Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients

inferred← citeshttps://doi.org/10.3389/fmicb.2020.00393openalex-snapshot

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

inferred← citeshttps://doi.org/10.3389/fmicb.2020.01835openalex-snapshot

Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits

inferred← citeshttps://doi.org/10.3389/fmicb.2021.678319openalex-snapshot

Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

inferred← citeshttps://doi.org/10.3389/fmicb.2022.889788openalex-snapshot

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1117965openalex-snapshot

Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1177947openalex-snapshot

Hybridization altered the gut microbiota of pigs

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1439652openalex-snapshot

The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet

inferred← citeshttps://doi.org/10.3389/fnagi.2022.820108openalex-snapshot

Gut Microbiota Composition and Metabolic Potential of Long-Living People in China

inferred← citeshttps://doi.org/10.3389/fnut.2025.1513973openalex-snapshot

Correlation study on gut microbiota and myosteatosis in patients with liver cirrhosis

inferred← citeshttps://doi.org/10.3389/fonc.2023.1218056openalex-snapshot

Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer

inferred← citeshttps://doi.org/10.3389/fphys.2016.00606openalex-snapshot

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

inferred← citeshttps://doi.org/10.3390/ani12172270openalex-snapshot

Comparison of Changes in Gut Microbiota in Wild Boars and Domestic Pigs Using 16S rRNA Gene and Metagenomics Sequencing Technologies

inferred← citeshttps://doi.org/10.3390/ijms26189206openalex-snapshot

Computational Metagenomics: State of the Art

inferred← citeshttps://doi.org/10.3390/metabo10030094openalex-snapshot

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

inferred← citeshttps://doi.org/10.3390/metabo11010055openalex-snapshot

Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

inferred← citeshttps://doi.org/10.3390/metabo9020022openalex-snapshot

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

inferred← citeshttps://doi.org/10.3390/microorganisms13071456openalex-snapshot

Disorders of Gut Microbiota and Plasma Metabolic Profiles May Be Associated with Lymph Node Tuberculosis

inferred← citeshttps://doi.org/10.3390/microorganisms8101563openalex-snapshot

RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing

inferred← citeshttps://doi.org/10.3390/microorganisms8121861openalex-snapshot

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

inferred← citeshttps://doi.org/10.3410/f.732860038.793582842openalex-snapshot

Faculty Opinions recommendation of Extensive impact of non-antibiotic drugs on human gut bacteria.

inferred← citeshttps://doi.org/10.34133/csbr.0002openalex-snapshot

annoSnake: A Snakemake Workflow for Taxonomic and Functional Annotation of Metagenomes and Metagenome-Assembled Genomes

inferred← citeshttps://doi.org/10.37501/soilsa/163080openalex-snapshot

Metagenomics approaches to understanding soil health in environmental research - a review

inferred← citeshttps://doi.org/10.53846/goediss-10594openalex-snapshot

Computational methods for prokaryotic (meta)genomic annotation and function prediction using horizontal information transfer

inferred← citeshttps://doi.org/10.6084/m9.figshare.13535033openalex-snapshot

Additional file 1 of Comparison of gut microbiota structure and Actinobacteria abundances in healthy young adults and elderly subjects: a pilot study

inferred← citeshttps://doi.org/10.6084/m9.figshare.13545509openalex-snapshot

Additional file 1 of Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

inferred← citeshttps://doi.org/10.6084/m9.figshare.13545515openalex-snapshot

Additional file 2 of Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

inferred← citeshttps://doi.org/10.6084/m9.figshare.13843693openalex-snapshot

Additional file 1 of Guild-based analysis for understanding gut microbiome in human health and diseases

inferred← citeshttps://doi.org/10.6084/m9.figshare.14053450openalex-snapshot

Additional file 2 of PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

inferred← citeshttps://doi.org/10.6084/m9.figshare.14344169openalex-snapshot

Additional file 1 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

inferred← citeshttps://doi.org/10.6084/m9.figshare.14344172openalex-snapshot

Additional file 2 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

inferred← citeshttps://doi.org/10.6084/m9.figshare.14344175openalex-snapshot

Additional file 3 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

inferred← citeshttps://doi.org/10.6084/m9.figshare.14385340openalex-snapshot

Additional file 1 of Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home

inferred← citeshttps://doi.org/10.6084/m9.figshare.21343282openalex-snapshot

Additional file 1 of Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics

inferred← citeshttps://doi.org/10.70675/317aa691za12fz4de9zac6az09fb8587337fopenalex-snapshot

Identification of key players in the gut microbiota based on a unified reference for a standardized quantitative metagenomics and metabolic analysis framework

inferred← citeshttps://doi.org/10.70675/c82d5d0ez084dz4ae6za044zfede1667bb46openalex-snapshot

Analyse de l'impact de Parvimonas micra sur les cellules coliques de l'hôte

inferred← citeshttps://doi.org/10.70675/e26ca2dcz0988z4fbfz8842zd84239740682openalex-snapshot

Étude du microbiote intestinal lié à l'hôte par métagénomique quantitative orientée clinique : relation phénotype – inflammation – microbiote dans la recto-colite hémorragique

inferred← citeshttps://doi.org/10.7507/1001-5515.202101083openalex-snapshot

[Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes].

inferred← citeshttps://doi.org/10.7554/elife.42693openalex-snapshot

Extensive transmission of microbes along the gastrointestinal tract

inferred← citeshttps://doi.org/10.7717/peerj.13529openalex-snapshot

Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3

inferred← citeshttps://doi.org/10.7717/peerj.9762openalex-snapshot

DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.