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SAMMate | A GUI tool for processing short read alignments in SAM/BAM format

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. 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.

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SAMMate classification

SAMMate specifications

Unique identifier:
Command line interface
Input data:
RNA-seq reads
Output data:
Localized reads to each annotated gene or un-annotated transcriptional unit in the SAM format and assembled mRNA sequences in FASTA format
Operating system:
Software type:
Restrictions to use:
Input format:
Output format:
Computer skills:

SAMMate distribution


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SAMMate support



  • Dongxiao Zhu <>


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Department of Computer Science, University of New Orleans, New Orleans, LA, USA; Tulane Cancer Center and Tulane Health Science Center, LA, USA; The Research Institute for Children, Children's Hospital, LA, USA

Funding source(s)

The Tulane Cancer Center Post-doctoral Matching Funds award; an NIH 1R21LM010137-01 grant; an NIH ARRA award (R01CA130752-02S1)

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