seekdeep¶

Description¶

The SeekDeep pipeline is intended for use on targeted amplicon sequencing data for haplotype frequency estimation for multiple samples from a population.

Environment Modules¶

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

Environment Variables¶

HPC_SEEKDEEP_DIR - installation directory
HPC_SEEKDEEP_BIN - executable directory

Citation¶

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

Hathaway, N. J., Parobek, C. M., Juliano, J. J., & Bailey, J. A. (2018). SeekDeep: Single-Base Resolution de Novo Clustering for Amplicon Deep Sequencing. Nucleic Acids Research, 46(4), e21. https://doi.org/10.1093/nar/gkx1201

Categories¶

biology, sequencing