Certain tools are recommended only for prokaryotes, such as Bowtie2. We recommend HISAT2 for aligner, StringTie for assembler, and DEseq2 for differential gene expression for prokaryotes. We do offer an additional tool, Cuffdiff, for differential gene expression. For eukaryotes, we offer Tophat2 or HISAT2 for assembly and Ballgown, Cuffdiff, and DESeq2 for differential gene expression. Our suggested pipelines are below: For prokaryotes - Bowtie2/HISAT2 ? StringTie ? DESeq2 (DESeq2 is based on gene counts). If you want to compare it with gene abundance, you can run Cuffdiff instead of DESeq2 at the last step. For Eukaryotes - HISAT2 ? StringTie ? DEseq2/Ballgown (you can run with Ballgown only if you want to compare these two different algorithms for differential gene expression). Though Cuffdiff can also work with eukaryotes but it is quite slow and too compute intensive for eukaryotes. So, Cuffdiff is only recommended if you have very few samples.