Software
These are tools we have released publicly. They are free to install and run.
We also maintain pipelines for breeding programs at Brandon that are not public. They stay inside the centre because they are connected to program data.
Open tools
nanoCAS Manuscript in preparation
Real-time detection and decision making during nanopore sequencing
Nanopore sequencing produces reads as it goes, but most analysis still waits for the run to finish. nanoCAS treats the run as a stream: it watches reads arrive, classifies them against a target database, and raises a detection as soon as there is enough evidence. For a field diagnostic, that can mean an answer in minutes rather than at the end of a flow cell.
It ships with a web interface so the person running the sample does not need a terminal.
Internal pipelines
Barley genomic selection In production at BRDC
Nextflow pipeline for genomic selection in barley
A genomic selection pipeline that any member of the barley breeding program can run without a bioinformatician. That was the design constraint.
If your program needs a pipeline or tool, get in touch.