Git Repos

WGS Processing

Process Illumina PE sequence data to call SNPs and small and large structural variants.

Accessory Scripts

Create variant matricies

TB specific

Call drug resistance
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

Deconvolute alignment files
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

Outlines for machine learning techniques