This depends on your dataset and your goals.
- If you are only analyzing data from one species and the reference transcriptome is well-annotated, you likely want to use Kallisto because it includes more features, including non-coding sequences and gene isoforms.
- If you are analyzing data from a species with a sparsely annotated reference, you may want Seq2Fun for better functional analysis.
- If you are analyzing data from multiple species, even if one or several have references, you may want to use Seq2Fun since this makes integrating the data and comparing results across species very easy.