swga: a primer design toolkit for selective whole genome amplification.
BACKGROUND
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.


METHODS
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.


BACKGROUND
ecl@mail.med.upenn.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.
Erik L
EL
Clarke
Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.|Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Sesh A
SA
Sundararaman
Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
Stephanie N
SN
Seifert
Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.
Frederic D
FD
Bushman
Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.|Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Beatrice H
BH
Hahn
Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
Dustin
D
Brisson
D000818:Animals; D017931:DNA Primers; D004331:Drosophila melanogaster / Q000382:microbiology; D005828:Genetics, Population / Q000379:methods*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020577:Wolbachia / Q000235:genetics
D017931:DNA Primers