sqp.png

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