Advanced topics 4: Pseudo-aligners (Lecture)

This is an alternative step INSTEAD of mapping, post-Alignment QC and quantification. Kallisto uses FastQ reads and a reference transcriptome (cDNA+ncRNA) to quantify transcripts using rapid pseudo-alignment along with bootstrap replicates to assess quantification inaccuracy. Kallisto is significantly faster than STAR or HISAT2 and has a small memory footprint. Kallisto generates transcript counts. Differential transcript expression is carried out using Sleuth which utilises bootstrap replicates.