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hybpiper website  

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.

Environment Modules

Run module spider hybpiper to find out what environment modules are available for this application.

System Variables

  • HPC_HYBPIPER_DIR - installation directory
  • HPC_HYBPIPER_BIN - executable directory
  • HPC_HYBPIPER_DOC - documentation directory
  • HPC_HYBPIPER_EXE - example directory


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

Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment. Applications in Plant Sciences, 4(7), 1600016. doi:10.3732/apps.1600016