Benchmark of scRNA-seq analysis tools

Jun 23, 2020

At the end of last year, I was curious to compare the results of a few single cell RNA-seq analysis tools, focusing on the generation of the transcript count matrix from the raw FASTQ files. The contenders are: 10x Genomics Cell Ranger, STARsolo, Alevin (Salmon), and kallisto. Even though this was done a while ago, and updates of the tools possibly influence the results, I thought it might be worth sharing anyway.