ArticleBioinformatics (Oxford, England)2017
swga: a primer design toolkit for selective whole genome amplification.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 49 citations in OpenAlex.
- Review
- Review
- Targeted sequencing ofmSystems · 2025Article
- Leveraging genomic insights from the neglected malaria parasites P. malariae and P. ovale using selective whole genome amplification (SWGA) approach.BMC genomics · 2025Article
- A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees.Scientific reports · 2025Article
- Population genomics of Plasmodium ovale species in sub-Saharan Africa.Nature communications · 2024Article
- A Novel and Rapid Selective Viral Genome Amplification and Sequencing Method for African Swine Fever Virus.Viruses · 2024Article
- Population genomics ofbioRxiv : the preprint server for biology · 2024Article
- Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection.The Journal of molecular diagnostics : JMD · 2024Review
- Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment.PLoS pathogens · 2024Review
- Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA.Scientific reports · 2024Article
- New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri.Scientific reports · 2024Article
- Article
- Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing.Scientific reports · 2023Article
- Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in Ouélessébougou, Mali.Scientific reports · 2023Article
- A fast machine-learning-guided primer design pipeline for selective whole genome amplification.PLoS computational biology · 2023Article
- Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.PLoS pathogens · 2023Article
- Development and Optimization of a Selective Whole-Genome Amplification To Study Plasmodium ovale Spp.Microbiology spectrum · 2022Article
- Genomic sequence capture of Plasmodium relictum in experimentally infected birds.Parasites & vectors · 2022Article
- Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
motivationPopulation genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets.
resultsHere, we present swga , a program that identifies primer sets for SWGA and evaluates them for efficiency and selectivity. We used swga to design and test primer sets for the selective amplification of Wolbachia pipientis genomic DNA from infected Drosophila melanogaster and Mycobacterium tuberculosis from human blood. We identify primer sets that successfully amplify each against their backgrounds and describe a general method for using swga for arbitrary targets. In addition, we describe characteristics of primer sets that correlate with successful amplification, and present guidelines for implementation of SWGA to detect new targets. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are freely available on https://www.github.com/eclarke/swga . The program is implemented in Python and C and licensed under the GNU Public License. CONTACT: ecl@mail.med.upenn.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.