ArticleCommunications biology2022
BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 22 citations in OpenAlex.
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.Frontiers in cellular and infection microbiology · 2025Article
- Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses.The Journal of infectious diseases · 2024Article
- Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.Journal of microbiology and biotechnology · 2024Article
- refMLST: reference-based multilocus sequence typing enables universal bacterial typing.BMC bioinformatics · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Long-Read Metagenomics and CAZyme Discovery.Methods in molecular biology (Clifton, N.J.) · 2023Article
- BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.Communications biology · 2022Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit's taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit's taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https://bugseq.com/academic .
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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.