2012
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
Preston M, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo J, Nosten F, Anderson T, Clark T. VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics 2012, 28: 2983-2985. PMID: 22976080, PMCID: PMC3496337, DOI: 10.1093/bioinformatics/bts557.Peer-Reviewed Original ResearchMeSH KeywordsGenetic VariationGenome, ProtozoanHigh-Throughput Nucleotide SequencingINDEL MutationPlasmodium falciparumPolymorphism, Single NucleotideSequence Analysis, DNASoftwareConceptsNext-generation sequencing dataUser-defined groupsGenomic regionsVariant call format filesSingle nucleotide polymorphismsDrug resistance genesSequence dataSequencing dataStructural variantsImportant antigenicSequence file formatsInformative markersPlasmodium falciparumDifferent continentsFile formatFormat fileUser manualReal timeAnalysis toolsGenesVariantsDeletionPolymorphismVarBFalciparumAnalysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O’Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo J, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara S, Marsh K, Jiang H, Su X, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White N, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail M, Turner D, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan J, Ferdig M, Amambua-Ngwa A, Conway D, Takala-Harrison S, Plowe C, Rayner J, Rockett K, Clark T, Newbold C, Berriman M, MacInnis B, Kwiatkowski D. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012, 487: 375-379. PMID: 22722859, PMCID: PMC3738909, DOI: 10.1038/nature11174.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBiodiversityGenome, ProtozoanGenotypeHigh-Throughput Nucleotide SequencingHumansMalaria, FalciparumPhylogenyPlasmodium falciparumPolymorphism, Single NucleotidePrincipal Component Analysis
2011
An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing
Auburn S, Campino S, Clark T, Djimde A, Zongo I, Pinches R, Manske M, Mangano V, Alcock D, Anastasi E, Maslen G, MacInnis B, Rockett K, Modiano D, Newbold C, Doumbo O, Ouédraogo J, Kwiatkowski D. An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing. PLOS ONE 2011, 6: e22213. PMID: 21789235, PMCID: PMC3138765, DOI: 10.1371/journal.pone.0022213.Peer-Reviewed Original ResearchMeSH KeywordsBurkina FasoDNA, ProtozoanGenomeHigh-Throughput Nucleotide SequencingHumansLeukocytesLymphocyte DepletionMaliParasitemiaPlasmodium falciparumSequence Analysis, DNAPopulation Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay
Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo J, Mangano V, Djimde A, Doumbo O, Kiara S, Nzila A, Borrmann S, Marsh K, Michon P, Mueller I, Siba P, Jiang H, Su X, Amaratunga C, Socheat D, Fairhurst R, Imwong M, Anderson T, Nosten F, White N, Gwilliam R, Deloukas P, MacInnis B, Newbold C, Rockett K, Clark T, Kwiatkowski D. Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay. PLOS ONE 2011, 6: e20251. PMID: 21673999, PMCID: PMC3108946, DOI: 10.1371/journal.pone.0020251.Peer-Reviewed Original ResearchMeSH KeywordsCloning, OrganismCulture TechniquesDNA, ProtozoanGenetic LociGenotypeHigh-Throughput Nucleotide SequencingLaboratoriesMalaria, FalciparumPlasmodium falciparumPolymorphism, Single NucleotideTime FactorsConceptsPopulation genetic studiesIllumina GoldenGateGenetic studiesSingle nucleotide polymorphism (SNP) discoveryLarge-scale population genetic studiesLaboratory clonesPopulation genetic diversityPopulation genetic analysesGenome sequencing projectsPlasmodium falciparum genomeTotal genomic DNAParasite population dynamicsMinor frequency allelesFalciparum genomePolymorphism discoveryGenetic diversitySequencing projectsWhole genomeP. falciparumGenetic analysisImportant phenotypesGenomic DNAHigh SNPPopulation dynamicsMultiple-clone infections