Overview
kallisto | bustools is a modular and efficient workflow designed for pre-processing single-cell RNA-seq data. It addresses key steps such as associating reads with their cells of origin, collapsing reads based on unique molecular identifiers (UMIs), and generating cell x gene count matrices. The workflow supports diverse technologies like 10x, inDrops, and Dropseq, along with feature barcoding data from CITE-seq, REAP-seq, and MULTI-seq. By providing customizable workflows, kallisto | bustools facilitates quantification, RNA velocity analysis, and QC reporting for single-cell RNA-seq data. Its modular design allows users to adapt it to new technologies and protocols, ensuring robust and scalable single-cell data analysis.