Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

Wang, Michael X.; Lou, Esther; Sapoval, Nicolae; Kim, Eddie; Kalvapalle, Prashant; Kille, Bryce; Elworth, R. A. Leo; Liu, Yunxi; Fu, Yilei; Stadler, Lauren B.; Treangen, Todd J.

doi:10.1101/2023.02.11.528155

Cited by 2 publications

(1 citation statement)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These tools take as input a set of reference genomes and a region of interest and attempt to find a set of primers such that the region of interest can be amplified in as many reference genomes as possible. In addition, PrimalScheme [44] and Olivar [58] have the option to find a near-minimal size set of primers such that the resulting amplicons would cover the entire genome, enabling amplicon-based WGS.…”

Section: Introductionmentioning

confidence: 99%

AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes

van Bemmelen,

Smyth,

Baaijens

2023

Preprint

View full text Add to dashboard Cite

Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights in microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions which maximize the number of lineages that can be distinguished. Here we present AmpliDiff, a computational tool that simultaneously finds such highly discriminatory genomic regions, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain mean absolute prediction errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data, and that primers designed by AmpliDiff continue to bind to genomes originating from months after the primers were selected. With AmpliDiff we provide an effective and efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.

show abstract

Section: Introductionmentioning

confidence: 99%

AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes

van Bemmelen,

Smyth,

Baaijens

2023

Preprint

View full text Add to dashboard Cite

show abstract

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes

Bemmelen,

Smyth,

Baaijens

2024

BMC Bioinformatics

View full text Add to dashboard Cite

Background Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights into microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought-after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions that maximize the number of lineages that can be distinguished. Results Here we present AmpliDiff, a computational tool that simultaneously finds highly discriminatory genomic regions in viral genomes of a single species, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data and that primers designed by AmpliDiff also bind to genomes sampled months after the primers were selected. Conclusions With AmpliDiff we provide an effective, cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.

show abstract

Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

Cited by 2 publications

References 38 publications

AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes

AmpliDiff: An Optimized Amplicon Sequencing Approach to Estimating Lineage Abundances in Viral Metagenomes

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes

Contact Info

Product

Resources

About