git clone https://github.com/malonge/RagTag
cd RagTag
python3 setup.py install

# correct contigs
ragtag.py correct ref.fasta query.fasta

# scaffold contigs
ragtag.py scaffold ref.fa ragtag_output/query.corrected.fasta

• Minimap2 or Nucmer
• Python 3 (with the following auto-installed packages)
  • numpy
  • intervaltree
  • pysam

Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17.

Many of the major algorithmic improvements relative to RaGOO's first release were provided by Aleksey Zimin, lead developer of the MaSuRCA assembler. This includes the use of read-mapping for misassembly validation as well as the use of alignment merging for improved scaffolding. Luca Venturini also suggested and initially implemented many feature enhancments, such as pysam integration.