r-make is a pipeline that processes RNA sequencing reads. r-make can generate the following output:

  • Aligned reads
  • SNP calls
  • Indels
  • Additionally, r-make estimates the expression levels for exons, genes, and splice junctions. In the process, it prints a range of quality metrics and statistics, such as coverage across gene body and percentage of mapping error, facilitating quality control and comparison with other samples. Managed by make, r-make is a wrapper for the creation of Makefiles, enabling massive parallelization of intricate analyses with minimal input from user.



    A previous iteration of this pipeline was developed in 2011. That version relied exclusively on GNU parallel. Work on that project has since been abandoned: as the cost of sequencing continues to decrease, the number of samples being sequenced continues to rise, making analysis increasingly cumbersome. Thus, a more sophisticated approach was warranted.

    r-make is inspired by Solexa's original pipeline. Solexa's original pipeline (and Illumina's current implementation of it) is powered by make. make automates the building of large, complicated processes by traversing dependency chains, allowing for unguided parallelization by abstraction. r-make picks up where Illumina leaves off. Specifically, r-make is, Illumina, meet the latest sequencing analysis tools, including star, bedtools, fastx-toolkit, and samtools.


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    Author: Paul Zumbo
    Staff Associate
    Sheng Li
    PhD Student
    Laboratory of Christopher E. Mason, Ph.D.
    Department of Physiol. & Biophys. &
    the Institute of Computational Biomed. @
    Weill Cornell Medical College of Cornell Univ.
    1305 York Avenue, Fl. 13, Box 140
    New York, NY 10021

    E-mail: paz2005@med.cornell.edu

    Web: here


    Name: Sheng Li

    E-mail: shl2018@med.cornell.edu

    p. zumbo