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npscarf website  

npScarf ( is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of positional information such as gene ordering and the detection of genes from mobile elements (plasmids and genomic islands).

Environment Modules

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

System Variables

  • HPC_NPSCARF_DIR - installation directory
  • HPC_NPSCARF_BIN - executable directory


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

Cao, M.D., Nguyen, H.S., et al. Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing. Nature Communications 8, Article number: 14515 (2017). doi:[10.1038/ncomms14515.]