SNV-FEAST: microbial source tracking with single nucleotide variants

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

• Publication year

  2023

• Venue

  bioRxiv

• Publication date

  2023-01-09

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1186/s13059-023-02927-8PMID 37121994PMCID 10150486
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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