Introduction

Cufflinks is a program in the gene sequencing field that is mainly used to calculate the gene expression volume and search for differentially expressed genes. Based on the comparison result of TopHat, the program calculates the FPKM value of isoform (of each gene) based on or not based on the GTF comment file of the reference genome, and provides the comment result in trascripts.gtf (assemble transcription groups). Cufflinks contains several main executable programs, such as Cufflinks, Cuffmerge, Cuffcompare, and Cuffdiff.

For more information, visit the official Cufflinks website.

Programming language: C++

Brief description: a program used to calculate the gene expression volume and search for differentially expressed genes.

Open source license: Boost Software License