ngs-python can fetch reads (according to the examples) analogous to vdb-dump. This would remove sra-toolkit from the pipeline and simplify some steps.
However, installing ngs-pyhton is not straightforward (https://github.com/ncbi/sratoolkit). It's not very complicated either, but enough to make step-by-step instruction longer than the Endovir README itself.
ngs-python can fetch reads (according to the examples) analogous to vdb-dump. This would remove sra-toolkit from the pipeline and simplify some steps.
However, installing ngs-pyhton is not straightforward (https://github.com/ncbi/sratoolkit). It's not very complicated either, but enough to make step-by-step instruction longer than the Endovir README itself.