Estimating differential expression with Kallisto and Sleuth
Kallisto is an RNA-Seq read aligner that uses a pseudoalignment algorithm, which allows it to map reads to a reference transcriptome without using traditional alignment methods such as Smith-Waterman or Needleman-Wunsch. Instead, it uses a k-mer index of the reference transcriptome to quickly and accurately quantify expression levels of transcripts. This allows Kallisto to run much faster than traditional aligners, making it a popular choice for large-scale RNA-Seq experiments.
The companion R package called Sleuth is a tool for analyzing the output from Kallisto. It allows users to perform differential expression analysis and identify transcripts that are differentially expressed between different samples or conditions. Sleuth uses a Bayesian framework to model the expression levels of transcripts and take into account technical variability in the data, such as sequencing depth and batch effects. The package also provides...
