ArticleGigaScience2025
Benchmarking short-read metagenomics tools for removing host contamination.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.Insect molecular biology · 2026Article
- Scalable assembly of Ascaris mitogenomes from whole-genome data reveals a novel clade.Scientific reports · 2026Article
- Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.Blood science (Baltimore, Md.) · 2026Review
- ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.Microbiology spectrum · 2026Article
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- Time-series dynamics and biocontrol potential of postharvest bacteria in litchi microbiota.Science China. Life sciences · 2026Article
- Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.Microbiome · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.Microbiology spectrum · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Review
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
- PIMENTO: a primer inference toolkit to facilitate large-scale calling of amplicon sequence variants.GigaScience · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.Bioinformatics (Oxford, England) · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.
resultsIn this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.
conclusionsOur findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.
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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.