Computational biology and genomics
In this post, I describe a simple workflow for identifying Omicron variants from some sequencing data shared by the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) and the Centre for Epidemic Response and Innovation (CERI). To follow the workflow, you need to have Docker installed and an Internet connection. To get started, run a container…
I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…
In my last post I outlined an approach for automatically creating reproducible documentation using GitHub Actions. I have now updated my Docker documentation using the same approach but without using a container because then I’d have to run Docker inside a Docker container (which is actually possible using GitLab’s CI/CD platform but I haven’t tried…