Software

A major aim of the Centre is the creation and distribution of software tools for the research community. Below is a selection of software (complete sets of tools are available from each member’s webpage).

 

Pathogen genomics

Screen Shot 2015-07-11 at 6.43.33 pmSRST2 – Genomic surveillance of bacterial pathogens (Holt and Inouye groups)
Genome Medicine 2014 | Code | Illumina BaseSpace | Behind the SRST2 project

Screen Shot 2015-07-11 at 6.29.20 pmISMapper – Identifying insertion sequences in bacterial genomes from short read sequence data (Jane Hawkey, Holt group)
BMC Genomics 2015 | Code

 

Genomic prediction of complex traits and diseases

Screen Shot 2015-07-11 at 6.24.51 pmmultiBLUP – Extension of Best Linear Unbiased Prediction (BLUP) for complex trait and disease prediction using SNP data (Doug Speed, Balding group)
Genome Research 2014 | Code

Screen Shot 2015-07-11 at 6.48.49 pmSparSNP – Regularized linear models of genetic data for phenotype prediction (Gad Abraham, Inouye group)
BMC Bioinformatics 2012 | Code

 

Statistical analysis of genomic data

Screen Shot 2015-07-11 at 6.18.43 pmflashpca – Rapid and scalable principal components analysis or canonical correlation analysis (Gad Abraham, Inouye group)
PLoS One, 2014 | Code

 

NetRep• NetRep – Rapid permutation-based approach for testing replication and preservation of gene co-expression networks (Scott Ritchie, Inouye group)
Cell Systems, 2016 | Code

Screen Shot 2015-07-11 at 6.23.32 pmIlluminus – Accurate genotype calling for the Illumina platform (Inouye group)
Bioinformatics, 2007 | Code

 

Statistical analysis of DNA profile evidence

Screen Shot 2015-07-11 at 6.35.46 pmlikeLTD – Computing likelihoods for DNA profile evidence, including complex mixtures (Balding group)
PNAS, 2013 | Code

 

Assembly graph visualisation & manipulation

Screen Shot 2015-07-11 at 6.16.44 pm
Bandage – Easy visualisation of assembly graphs (Ryan Wick, Holt group)
Bioinformatics, 2015 | Code