I have downloaded FASTQ files from a single cell experiment that used SMART-seq2. As you know, this pipeline generates 2 read files per single cell. I am able to allign the reads using HISAT2, however, I am not sure about the appropriate tool to merge the different counts together and produce a single cell matrix.
These are our available tutorials for single-cell analysis. Not all tools are covered but maybe helps you to get oriented? Most are mapping some external publication or original author resources to the Galaxy version’s of tools, along with general text manipulations tools for intermediate steps (shell tools, etc). Those can be a reference for the “how-to” when custom translating methods from other sources, or when developing your own.