ArticlePLoS computational biology2021
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome.eLife · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- CAMP: a modular metagenomics analysis system for integrated multistep data exploration.NAR genomics and bioinformatics · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.NAR genomics and bioinformatics · 2025Article
- Article
- Centriflaken: An automated data analysis pipeline for assembly and in silico analyses of foodborne pathogens from metagenomic samples.PloS one · 2025Article
- Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.Applied and environmental microbiology · 2024Article
- Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of AllMicroorganisms · 2024Article
- Metagenome-assembled genome sequences of two bacterial species from polyvinyl alcohol-degrading co-colonies.Microbiology resource announcements · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG.F1000Research · 2024Article
- Article
- Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources.Microorganisms · 2023Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.GigaByte (Hong Kong, China) · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.