Bascet is a complete solution for single-cell analysis, with focus on microbial analysis. It is however design to also do RNA-seq, ATAC-seq (you-name-it), agnostic from the instrument used. It has also been designed to analyze large numbers of bulk samples in a manner analogous to single-cell analysis (i.e. with a focus on clustering and data-driven analysis).
Bascet is an advanced command-line tool aimed primarily to be used through the Zorn R library, which offers multi-node compute capability and ease of use.
Most users will prefer to use Zorn. For more information, follow this link: https://henriksson-lab.github.io/zorn/