Simple bacterial assembly and annotation pipeline

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Assembly and intrahost/low-frequency variant calling for viral samples

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Links to slides for rstudio::conf 2019

Useful bash one-liners for bioinformatics.