Research fellow at the University of Warwick and the NIHR Health Protection Research Unit (HPRU) in gastrointestinal infections
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KmerAperture
KmerAperture PublicExtract SNPs and accessory differences in closely related bacterial genomes from k-mers
Python 6
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BactStream
BactStream PublicDownload bacterial genome .fastq files and produce annotated variants one genome at a time
Python
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BactVar
BactVar PublicMap whole bacterial short reads with BWA and call variants with GATK. Outputs SnpEff annotated variants and a whole-genome alignment
Python
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