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]

When mapping reads with bwa mem, if you use the -M flag, the split reads are maked as secondary and they will not be used by smoove to get split-read support. This will cause all the variants in your VCF file to have SR=0. If you don’t use split-read support... [Read More]