ArticleNAR genomics and bioinformatics2022
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Article
- Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.Microbiology spectrum · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA.Microbiology resource announcements · 2026Article
- A novelApplied and environmental microbiology · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Distinct prokaryotic gut microbiome and proviral-immune axes of pathophysiology in Sickle Cell Disease.bioRxiv : the preprint server for biology · 2026Article
- Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.Scientific data · 2026Article
- Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agentMicrobiology spectrum · 2026Article
- Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.Communications biology · 2026Article
- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
- 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
- Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at Äspö, Sweden.Communications biology · 2026Article
- To multicellularity and back again: Description of two new coccoid genera (Portococcus gen. nov. and Pseudanabaenococcus gen. nov.) in the basal "filamentous" order Pseudanabaenales, Cyanobacteria.Journal of phycology · 2026Article
- Article
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install-all dependencies are provided within containers-portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All codes are hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.
Identifiers
What OpenQuestion holds
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.