ArticleNature methods2024
Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.Microbiology spectrum · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- nTChap: an accurate method for polyploid haplotype reconstruction.BMC genomics · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Article
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
- Metagenomics and its impact on environmental and therapeutic microbiology.Archives of microbiology · 2025Review
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- Genomic characterisation of recurrent Mycobacterium avium isolates from chronically infected patients reveals patterns of within-host evolution.Genome medicine · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
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Authors and funding
5 authors.
Funding
Abstract
Bacterial species in microbial communities are often represented by mixtures of strains, distinguished by small variations in their genomes. Short-read approaches can be used to detect small-scale variation between strains but fail to phase these variants into contiguous haplotypes. Long-read metagenome assemblers can generate contiguous bacterial chromosomes but often suppress strain-level variation in favor of species-level consensus. Here we present Strainy, an algorithm for strain-level metagenome assembly and phasing from Nanopore and PacBio reads. Strainy takes a de novo metagenomic assembly as input and identifies strain variants, which are then phased and assembled into contiguous haplotypes. Using simulated and mock Nanopore and PacBio metagenome data, we show that Strainy assembles accurate and complete strain haplotypes, outperforming current Nanopore-based methods and comparable with PacBio-based algorithms in completeness and accuracy. We then use Strainy to assemble strain haplotypes of a complex environmental metagenome, revealing distinct strain distribution and mutational patterns in bacterial species.
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