Verkko¶
Description¶
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. Verkko is Finnish for net, mesh and graph. Verkko uses Canu to correct remaining errors in the HiFi reads, builds a multiplex de Bruijn graph using MBG, aligns the Oxford Nanopore reads to the graph using GraphAligner, progressively resolves loops and tangles first with the HiFi reads then with the aligned Oxford Nanopore reads, and finally creates contig consensus sequences using Canu's consensus module.
Environment Modules¶
Run module spider verkko to find out what environment modules are available for this application.
Environment Variables¶
- HPC_VERKKO_DIR - installation directory
- HPC_VERKKO_BIN - executable directory
Categories¶
genomics