Year: 2017
Type: article
Abstract: MOTIVATION: Population 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. RESULTS: Here, 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: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Institution: University of Pennsylvania
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,989
Awards: G1214792496, G1268242786, G1388710674, G2119626930, G2963284521, G4762734956, G6811903907, Causes and consequences of ospC variation in Borrelia burgdorferi to Lyme disease, Great Ape Reservoirs of Human Malaria, Exploiting the antigenic conservation of the Env trimer apex across primate lentiviral lineages for AIDS vaccine design, G845143523, G9000000688, G9000001257, G9000006503, G9000042340, G9000058976, G9000072701, G9000106515, G9000141949, G9000148241, G9000190699, G9000266210
OpenAlex ID: W2592264164