ArticleGenome biology2020
Metalign: efficient alignment-based metagenomic profiling via containment min hash.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.npj antimicrobials and resistance · 2025Article
- CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software.Nucleic acids research · 2025Article
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.Science advances · 2024Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
- CAIM: coverage-based analysis for identification of microbiome.Briefings in bioinformatics · 2024Article
- CAIM: Coverage-based Analysis for Identification of Microbiome.bioRxiv : the preprint server for biology · 2024Article
- RUBICON: a framework for designing efficient deep learning-based genomic basecallers.Genome biology · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.Bioinformatics (Oxford, England) · 2024Article
- Fulgor: a fast and compact k-mer index for large-scale matching and color queries.Algorithms for molecular biology : AMB · 2024Article
- Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts.Frontiers in veterinary science · 2024Article
- A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review.Frontiers in microbiology · 2024Review
- Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.Genome research · 2023Article
- Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.Genome research · 2023Article
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Authors and funding
5 authors.
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Abstract
Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignment-based metagenomic profiling. We use a novel containment min hash approach to pre-filter the reference database prior to alignment and then process both uniquely aligned and multi-aligned reads to produce accurate abundance estimates. In performance evaluations on both real and simulated datasets, Metalign is the only method evaluated that maintained high performance and competitive running time across all datasets.
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