ArticleGenome research
Analyzing rare mutations in metagenomes assembled using long and accurate reads.
Article in Genome research. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.Microorganisms · 2024Review
- Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.Nature methods · 2024Article
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
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Authors and funding
3 authors.
Funding
Abstract
The advent of long and accurate "HiFi" reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling "complete metagenomics" studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever mutate, and to identify co-occurring groups of mutations. However, the problems of identifying rare mutations in MAGs, estimating the false-discovery rate (FDR) of these identifications, and phasing identified mutations remain open in the context of HiFi data. We present strainFlye, a pipeline for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs' growth dynamics.
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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.