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npScarf is a tool for assembly scaffolding and gap filling suitable for smaller genomes already assembled with short reads. It takes advantage of the long reads Oxford Nanopore streaming of sequencing result to continuously analyse how the new sequences generated improved the assembly by monitoring key metrics. Once sufficient contiguity or other metrics deemed suitable have been achieved, the long read sequencing can be stopped and hence saves time and money.


Sequence assembly


  • Operation: Genome assembly; Scaffolding
  • Input: FASTQ
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: -
  • License: BSD-like license
  • Cost: -
  • Version name: -
  • Credit: National Health and Medical Research Council; Australian Research Council
  • Contact: -
  • Collection: -


Cao MD, Nguyen SH, Ganesamoorthy D, Elliott AG, Cooper MA, Coin LJ "Scaffolding and completing genome assemblies in real-time with nanopore sequencing." Nature Communications
PMID: 28218240
PMCID: PMC5321748

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