SAMMate

Introduction

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


Pipeline

 assemblySAM
 ==========>==========================>=============================>>
        
                                                                                                                                                                                                     
                                                                                                                                   

                                                  =============>==================>>
                                                  SAMMate



Contributors

• Dongxiao Zhu: Associate Professor, Department of Computer Science, Wayne State University (Principal Investigator), email:  dzhu@wayne.edu, website: http://www.cs.wayne.edu/dzhu/
• 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)