Methods and tools

exSTRa

exSTRa identifies individuals with repeat expansions, a type of genetic mutation that leads to human genetic disorders such as Huntington’s disease, Friedreich’s ataxia and CANVAS. 

superSTR

superSTR identifies samples with unusual repeat motif distributions using an ultra-fast method. It is alignment free and can be used on sequencing data from any species, including RNAseq.

TBtyper (R package)

TBtyper is an exquisitely sensitive TB strain detection method which can tease apart mixed TB infections. It identifies membership to lineages.

RUVcorr (R package)

RUVcorr allows users to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data. 

XIBD (R package)

XIBD performs pairwise identity by descent analysis on the X chromosome and autosomes using SNP genotype data. 

isoRelate (R package)

isoRelate performs pairwise identity by descent analysis on haploid recombining organisms in the presence of multiclonal infections using SNP genotype data. 

cavalier 

cavalier (Candidate Variant List Evaluation Report) is an R package designed to assist with filtering and interpreting candidate variants in human whole exome or whole genome sequencing data. Information from a variety of sources is automatically combined and used to generate a presentation ready results, suitable for clinical reporting and discussion. 

For all tools please visit the Bahlo Lab GitHub page.

Media and resources

• AMSI Careers Maths Delivers “Gene Mapping” – Professor Melanie Bahlo
• Fighting malaria with maths - Dr Lyndal Henden, AMSI CHOOSEMATHS ambassador
• Analysing big data relating to gene expression - Dr Saskia Freytag, 3RRR radio Einstein A Go Go
• A genetic treasure map: new research into MacTel – Anna Quaglieri, Roberto Bonelli