SSR pipeline

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ssr_pipeline website  

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data.

Required Modules


  • ssr_pipeline

System Variables

  • HPC_SSR_PIPELINE_DIR - installation directory


If you publish research that uses ssr_pipeline you have to cite it as follows:

Miller, M.P., Knaus, B.J., Mullins, T.D., and Haig, S.M., 2013, SSR_pipeline—Computer software for the identification of microsatellite sequences from paired-end Illumina High-Throughput DNA sequence data (ver. 1.1, February 2014): U.S. Geological Survey Data Series 778.