hapdup

Description

hapdup website

HapDup takes as input a haploid long-read assembly, such as produced with Flye or Shasta. Currenty, ONT reads (Guppy 5+ recommended) and PacBio HiFi reads are supported.

Environment Modules

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

Environment Variables

• HPC_HAPDUP_DIR - installation directory
• HPC_HAPDUP_BIN - executable directory

Citation

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

Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Gunjan Baid et al. "Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks." bioRxiv (2021). doi:10.1101/2021.03.04.433952

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8

Categories

phylogenetics, biology