ReviewNature protocols2022
Metagenome analysis using the Kraken software suite.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 458 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
458 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis.Journal of molecular evolution · 2026Pooled it
- Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.BMC psychiatry · 2025Trial
- A machine-learning informed circulating microbial DNA signature for early diagnosis of esophageal adenocarcinoma.Gut microbes · 2026Article
- Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.Gut microbes · 2026Article
- Optimized approaches to profile low biomass DNA and RNA virome in the upper respiratory tract of beef cattle.Animal microbiome · 2026Article
- Article
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health.Environmental microbiology reports · 2026Article
- Polymeric alpha-1 antitrypsin perturbs Paneth cell proteostasis and exacerbates intestinal inflammation.Signal transduction and targeted therapy · 2026Article
- Urban Tree Pathogens: The Impact of Neofusicoccum luteum on Araucaria heterophylla (Norfolk Island Pine).Environmental management · 2026Article
- Antimicrobial-resistant organism carriage and metagenomic characterization of the microbiome and resistome in veterinary workers.Veterinary research communications · 2026Article
- Gut single-microbe landscape in patients with major depressive disorder and bipolar disorder.Molecular psychiatry · 2026Article
- Impacts of climate extremes on plant pathogens, microbiomes and plant health.Nature reviews. Microbiology · 2026Review
- Emergence ofASM case reports · 2026Article
- Endogenous CRISPR-Based Removal of Tetracycline Resistance in Bifidobacterium animalis subsp. lactis Through a Safe-by-Design Approach.Microbial biotechnology · 2026Article
- Comparative genomic characterization and antimicrobial resistance of bacteremia-causingMicrobiology spectrum · 2026Article
- Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams.JDS communications · 2026Article
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.Journal of advanced research · 2026Article
- Article
398 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.
Indexed as
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.