SAMMate specifications


Unique identifier OMICS_01264
Name SAMMate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA-seq reads
Input format FASTQ
Output data Localized reads to each annotated gene or un-annotated transcriptional unit in the SAM format and assembled mRNA sequences in FASTA format
Output format SAM, FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Dongxiao Zhu <>

SAMMate article

SAMMate citation

PMCID: 3699530

[…] saved in a sam format., based on the alignment results of all the samples, expression abundance estimation was conducted at both gene and isoform levels using ensembl astd database (version 60). sammate (, free graphical user interface (gui) software, was employed for gene and isoform quantification. for isoform quantification, we applied the method, raem […]

SAMMate institution(s)
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
SAMMate 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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