Plotting my training data because I'm a nerd and a jock.

Nextflow pipeline to align, variant call, phase and annotate long read ONT and/or pacbio HiFi data

A collection of tasty script nibs I like and don't want to loose

A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.

Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.

Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).

Analysis documentation for part of the reference genome assembly of the humble guinea pig. Oxford Nanopore Technologies (ONT) pore-c data.

An initial place to collate projects associated with the Human Genomics group at ESR

Analysis documentation for research into human adipose nanopore methylation. Oxford Nanopore Technologies (ONT), human, adipose, germline, adaptive sampling data.

Minimal tests for the amount of compute resources required for analysing human genomics datasets at ESR.

Recipes for containerised software.

Wrapper scripts to automate some aspects of running human_genomics_pipeline and vcf_annotation_pipeline.

Small non-coding RNA analysis template for analysing Illumina small RNAseq data.

Analysis template for analysing Illumina RNAseq data.

An R Shiny app that presents a few key results of my MSc thesis.

Files used to compile my MSc thesis.

A place for talks, blurbs, bios etc related to work at ESR.

Snakemake workshop for RezBaz2020.

Helping a colleague reviewing/testing the seattleflu/assembly pipeline.

A review of the current pipelines/tools available for analysing DNA/RNA data.

Benchmarking parabricks on NVIDIA A100's on NeSi.

A bit of starter code to help a colleague get started wrangling and extracting summary statistics from a road crash dataset in R.

Trying to help a colleague get a 16s-rRNA-Sanger snakemake pipeline working.

Documentation for various ESR projects.

A simple singularity recipe for Madeline 2.0 Pedigree Drawing Engine.

Files used to compile a gitbook version of my MSc thesis.