Amplicon Analysis I

Eduardo Pareja-Tobes; Raquel Tobes

doi:10.20944/preprints201909.0171.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

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.

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

Computer Science and Mathematics, Mathematical and Computational Biology

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Amplicon Analysis I

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