A fast machine-learning-guided primer design pipeline for selective whole genome amplification

Abstract

Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales – precisely the scales at which these processes occur – microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluate strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime from weeks to minutes. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluated the novel swga2.0 pipeline by designing primers sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.

Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies

“…We used the program swga [ 16 ] to generate a list of 172 candidate primers that preferentially bind to the Leishmania braziliensis reference genome (MHOM/BR/75/M2904 2019) over a complex background genome that consisted of human (GCA_000001405.28), Staphylococcus aureus (GCA_000746505.1), and Streptococcus pyogenes (GCA_000006785.2). We scored these candidate primers and designed primer sets using an updated machine-learning-guided and thermodynamically-principled version of the SWGA algorithm, swga2.0 [ 31 ](software available at https://anaconda.org/janedwivedi/soapswga ). Overall, 23 unique 8-mer primers with the highest evaluation scores calculated from swga2.0 were generated (Integrated DNA Technologies).…”

“…We used the improved SWGA algorithm, swga2.0, which employs machine learning to design primer sets that preferentially bind to a target genome, compared to one or more background genomes ( [31]; see Methods). We used L. braziliensis (MHOM/BR/75/M2904 2019) as the target genome and the human genome as background.…”

Selective whole-genome amplification reveals population genetics ofLeishmania braziliensisdirectly from patient skin biopsies

“…We used the program swga [16] to generate a list of 172 candidate primers that preferentially bind to the Leishmania braziliensis reference genome (MHOM/BR/75/M2904 2019) over a complex background genome that consisted of human (GCA_000001405.28), Staphylococcus aureus (GCA_000746505.1), and Streptococcus pyogenes (GCA_000006785.2). We scored these candidate primers and designed primer sets using an updated machine-learningguided and thermodynamically-principled version of the SWGA algorithm, swga2.0 [31](software available at https://anaconda.org/janedwivedi/soapswga). Overall, 23 unique 8-mer primers with the highest evaluation scores calculated from swga2.0 were generated (Integrated DNA Technologies).…”