HybPiper¶

Description¶

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.

Environment Variables¶

HPC_HYBPIPER_DIR - installation directory
HPC_HYBPIPER_BIN - executable directory
HPC_HYBPIPER_DOC - documentation directory
HPC_HYBPIPER_EXE - examples directory

Citation¶

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., & 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), Article 1600016. https://doi.org/10.3732/apps.1600016

Categories¶

biology, phylogenetics