Software
Most of what the lab builds is released openly. The tools below fall into two groups: things anyone can install and run, and internal pipelines built for specific breeding programs at Brandon that we are working towards releasing.
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 the evidence is there — which for a field diagnostic 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.
MICAS Released
MinION classification and alerting system
The precursor to nanoCAS. Watches a MinION run, classifies reads against a configured set of targets, and alerts when one appears.
genoassist Released
Assemble, annotate, then choose
Genome assembly rarely has one right answer. genoassist runs a genome through multiple assembly and annotation routes and reports the properties of each result side by side, so the choice of assembly is made on evidence rather than on whichever tool was run first.
BiocSwirl Released
Learn Bioconductor workflows inside R
Interactive swirl courses that teach bioinformatics workflows in R and Bioconductor from inside the R console, so learners never have to context-switch between a tutorial and the thing they are learning.
Internal pipelines
Barley genomic selection In production at Brandon
Run by the breeding program, not for it
A genomic selection pipeline that any member of the barley breeding program can run with minimal training. The point of the design was that it should not require a bioinformatician to be free that week.
Wheat pedigree explorer In development
See a trait move through the crosses
An interactive pedigree view for wheat: pan through the pedigree, colour by trait, overlay KASP marker calls, and check visually whether a marker is driving a phenotype or merely travelling near it. Built on the graph representation described under Research.
Variant calling and QTL workflows Ongoing
Atomic, documented, transferable
Standard workflows for variant calling, GWAS and QTL mapping, written to be run independently and documented well enough that a discrete task can move to whoever has capacity — across the Brandon and Morden groups rather than within one of them.
If one of these is close to something you need but not quite right, say so. Most of them exist because someone asked.