I didn’t find an easy way to visualise CNAs from the EPI2ME wf-human-variation, so I wrote a simple Rshiny app to do it. It reads the output files from the workflow and displays the CNAs in an interactive plot. [Read More]

Here I share a script to automatically query the ensembl rapid release page for homologues (from a couple of species) of a given list of genes (from one species). [Read More]

Writting a Snakemake pipeline can be quite repetitive, you add rule after rule and they all follow the same format. To make it easier and faster to write a Snakemake pipeline I created this snippets file in Visual Studio Code (it may also be possible in other editors). Snippets work... [Read More]

While trying to use this snakemake Freebayes wrapper I came across the following error: [Read More]

A pipeline for creating an assembly from nanopore reads. It creates an assembly, does scaffolding with long reads and polishing with short reads. It also does variant calling with short reads and with long reads separately. In addition, this pipeline computes busco scores before and after polishing. From this pipeline... [Read More]