Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

摘要

The main step in most RNA sequencing (RNA-seq) analyses is the alignment of sequencing reads against the reference genome or transcriptome to find the location from which the reads originate. The positional information of the reads, together with the sequences of the reads themselves, forms the basis from which many different downstream analyses can be performed, such as gene expression analysis, variant calling, and novel isoform identification. The read alignment step is typically one of the most time consuming steps during RNA-seq analysis due to the complex algorithm utilised during the read alignment process. There have been a number of recently published tools which are designed to skip this expensive step through the use of pseudoalignment methods, such as kallisto [ ] and Salmon [ ]. However, these tools are designed specifically for read quantification and therefore are not applicable to other types of downstream analyses.