ArticleBMC bioinformatics2020
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed, 192 citations in OpenAlex.
- Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.BMC biology · 2023Trial
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.Gut microbes · 2026Article
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Steroid hormones produced by coral-associated Endozoicomonas influence coral immune response during thermal stress.Nature microbiology · 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
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- Microbiome signatures for detection of colorectal lesions in population-based FIT screening.Nature communications · 2026Article
- Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.Scientific reports · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.Microbiome · 2026Article
- A framework for reproducibly managing coupled research software and data assets based on shared transformation functions.Patterns (New York, N.Y.) · 2026Article
- StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.Bioinformatics (Oxford, England) · 2026Article
- Rafts of change: microbial and functional dynamics in simulatedApplied and environmental microbiology · 2026Article
- Plant and soil transcriptomics reveal the consequences of bioaugmentation of co-contaminated soil with Pseudomonas qingdaonensis ZCR6 during bacteria-assisted phytoremediation.Applied microbiology and biotechnology · 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
- Metabolic transitions along a moisture gradient in a poly-extreme high-altitude desert ecosystem within the Atacama Desert.Environmental microbiome · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.Animal microbiome · 2026Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundMetagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.
resultsHere we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.
conclusionsATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.
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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.