Article

Strain tracking with uncertainty quantification

2023-01-26

Abstract excerpt

The ability to detect and quantify microbiota over time has a plethora of clinical, basic science, and public health applications. One of the primary means of tracking microbiota is through sequencing technologies. When the microorganism of interest is well characterized or known a priori , targeted sequencing is often used. In many applications, however, untargeted bulk (shotgun) sequencing is more appropriate;...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: c8558054-8160-5838-ae52-142742dcf299
DOI: 10.1101/2023.01.25.525531

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Strain tracking with uncertainty quantificationDOI 10.1101/2023.01.25.525531Read

Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantationSemantic proximity Read

Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome.Semantic proximity Read

Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.Semantic proximity Read

Enhanced metagenomics-enabled transmission inference with TRACSSemantic proximity Read

Scalable microbial strain inference in metagenomic data using StrainFactsSemantic proximity Read

Microbial source tracking using metagenomics and other new technologiesSemantic proximity Read

Quantifying Metagenomic Strain Associations from Microbiomes with AnpanSemantic proximity Read

Benchmarking strain-level profiling of <i>Escherichia coli</i> in short-read gut metagenomesSemantic proximity Read

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communitiesSemantic proximity Read

Metax: A Coverage-Informed Probabilistic Framework for Accurate Cross-Domain Taxon ProfilingSemantic proximity Read

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGCSemantic proximity Read

ZipStrain Enables Rapid and Precise Strain-Resolved MetagenomicsSemantic proximity Read