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Git Repos

WGS Processing
Process Illumina PE sequence data to call SNPs and small and large structural variants.
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Accessory Scripts
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Create variant matricies
TB specific
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Call drug resistance
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Comprehensive in silico genotyping

RNAseq Processing
Aligned to one genome, then the unaligned sequences may be aligned to a second genome. This is useful when complex, mixed clinical samples have been sequenced.
Accessory Scripts
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Deconvolute alignment files
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Call SNPs and small structural variants

GWAS scripts
Using a variant matrix and a phenotype perform GWAS using a linear, logistic, ordinal regression or efficient mixed-model association. Epistatic interactions can be included.
Accessory Scripts
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Outlines for machine learning techniques
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