fabricebesnard/snpeff repository overview

This docker image contains the annotation program 'snpEff' [https://pcingola.github.io/SnpEff/⁠], in a custom installation with a few pre-built databases of popular model organisms in biology. Indeed, when running snpEff in a docker, it is not always possible to download a species database (and store them in the default /data folder), because the running container is protected from writing by the user. To avoid this issue, this docker image already contains a few databases for some species of interest.

Unless otherwise stated in the docker tag, the available species databases in this docker are:

• Arabidopsis_thaliana
• Zea_mays
• Physcomitrella_patens
• Populus_trichocarpa
• Drosophila_melanogaster
• Caenorhabditis_elegans
• Caenorhabditis_briggsae
• Saccharomyces_cerevisiae
• Schizosaccharomyces_pombe

If the pre-built database of you favorite species has no been pre-downloaded, you can build your own docker with relevant species databases using this procedure: https://github.com/fabfabBesnard/Parallel-Variant-Calling/tree/main/dockersnpeff⁠

In the docker tagged as repeat-aware_latest, adds-on are included in order to run a process of the Parallel-Variant-Calling⁠ nextflow pipeline in the final container:

• an additional script and corresponding python environment
• bedtools 2.30.0⁠