NextDenovo¶

Description¶

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, please use NextPolish.

Environment Modules¶

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

Environment Variables¶

HPC_NEXTDENOVO_DIR - installation directory
HPC_NEXTDENOVO_BIN - executable directory

Citation¶

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

Hu, J., Wang, Z., Sun, Z., et al. (2024). NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology, 25(1), 1–19. https://doi.org/10.1186/s13059-023-03197-9

Categories¶

phylogenetics