Sleuth is an R-package for k-mer isoform differential analysis tool for Rna-Seq Kallisto. Unlike Kallisto, Sleuth is not published in any respectful journal. It's not even listed on Bioconductor.
Both edgeR and DESeq2 have been tested extensively, so I'm confident working with them. However, my experience with Sleuth is mixed; the fold-change values it reports are suspicious.
Q: What does the Bioinformatics community think about Sleuth? Would you like it be part of your pipeline?