Scruff

Scruff

Scruff (Single Cell RNA-Seq UMI Filtering Facilitator) is a package for processing single cell RNA-seq (scRNA-seq) FASTQ reads generated by CEL-Seq and CEL-Seq2 protocols. It demultiplexes scRNA-seq FASTQ files, aligns reads to reference genome using Rsubread, and generates UMI filtered count matrix.​​

Important Links to this Software

Github