Preprint Article Version 1 This version is not peer-reviewed

Amplicon Analysis I

Version 1 : Received: 12 September 2019 / Approved: 16 September 2019 / Online: 16 September 2019 (16:45:10 CEST)

How to cite: Pareja-Tobes, E.; Tobes, R. Amplicon Analysis I. Preprints 2019, 2019090171 (doi: 10.20944/preprints201909.0171.v1). Pareja-Tobes, E.; Tobes, R. Amplicon Analysis I. Preprints 2019, 2019090171 (doi: 10.20944/preprints201909.0171.v1).

Abstract

Here we present 1. a model for amplicon sequencing 2. a definition of the best assignment of a read to a set of reference sequences 3. strategies and structures for indexing reference sequences and computing the best assign- ments of a set of reads efficiently, based on (ultra)metric spaces and their geometry The models, techniques, and ideas are particularly relevant to scenarios akin to 16S taxonomic profiling, where both the number of reference sequences and the read diversity is considerable.

Subject Areas

Bioinformatics; NGS; DNA sequencing; DNA sequence analysis; amplicons; ultrametric spaces; indexing

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