Dongxiao Zhu
Tin Nguyen

Guorong Xu
Nan Deng

Kristen Johnson
Zhiyu Zhao

Getting help

If you have questions and comments, please joint  SAMMate Group or email to

News and updates

5/11/2013 assemblySAM 1.1 is released.

11/10/2012 SAMMate 2.7.4 is released.

10/10/2012 SAMMate 2.7.3 is released.

8/9/2012 SAMMate 2.7.2 is released.


SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.
  • The inputs are RNA-seq reads in the .fastq format.
  • Two kinds of outputs: (1). Localized reads to each annotated gene or un-annotated transcriptional unit in the SAM format. (2). Assembled mRNA sequences in .fasta format.  
Download assemblySAM 1.1
Download Simulation Data and Scripts for SPATA

SAMMate, a GUI RNA-seq quantification pipeline, allows biomedical researchers to quickly process fasta/fastq and SAM/BAM files, and is compatible with both single-end and paired-end sequencing technologies. SAMMate implements the following two transcript quantification algorithms developed in our research group:
  • Read Assignment via Expectation Maximiation (RAEM) (Deng et al. Nucleic Acids Research doi: 10.1093/nar/gkr042).
  • Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts (SASeq). (Nguyen et al. arXiv:1208.3619)
Download SAMMate 2.7.4
Download Simulation Data and Scripts for SASeq





  • Dongxiao Zhu: Associate Professor, Department of Computer Science, Wayne State University (Principal Investigator), email:, website:
  • Nan Deng: PhD student, Department of Computer Science, Wayne State University
  • Tin Nguyen (previous contributor), PhD student, Department of Computer Science, Wayne State University
  • Guorong Xu (previous contributor, now at Baylor Dallas)
  • Kristen Johnson (previous contributor, now at Purdue)
  • Zhiyu Zhao (previous contributor, now at UT Southwestern Medical Center)