ArticleBMC bioinformatics2020
SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.
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 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.International journal of molecular sciences · 2026Trial
- From onset to healing: temporal dynamics of microbial communities pinpoint Midichloria-like organism's key role in the development of the fish skin disease red mark syndrome.Animal microbiome · 2026Article
- KEGG-Based Functional Signatures Complement Taxonomic Profiles Associated with Spontaneous Decolonisation of Carbapenem-ResistantInternational journal of molecular sciences · 2026Article
- Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.FEMS microbiology ecology · 2026Article
- Metagenomics and metatranscriptomics of prokaryotic and fungal microbiomes in produced water associated with petroleum degradation and pipeline corrosion from an oil terminal in Brazil.World journal of microbiology & biotechnology · 2026Article
- Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.FEMS microbiology ecology · 2026Article
- Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.Environmental microbiome · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.Scientific reports · 2026Article
- Linking metagenomic insight to cultivable microbes: isolation of a vitamin BBMC microbiology · 2026Article
- Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.Journal of translational medicine · 2026Article
- Halophilic Anaerobic Cultures Enriched with COMicrobial ecology · 2026Article
- Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.Frontiers in microbiology · 2026Article
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- Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.BMC microbiology · 2025Article
- An Innovative Binding-Protein-Based dsRNA Extraction Method: Comparison of Cost-Effectiveness of Virus Detection Methods Using High-Throughput Sequencing.Molecular ecology resources · 2025Article
- Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics.Foods (Basel, Switzerland) · 2025Article
- Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?Molecular ecology · 2025Article
- Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of theMicrobiology spectrum · 2025Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.
resultsHere we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.
conclusionsAltogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.
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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.