RagTag 1.1.0

Fast reference-guided genome assembly scaffolding

Getting Started

# install with conda
conda install -c bioconda ragtag

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

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

# scaffold with multiple references
ragtag.py scaffold -o out_1 ref1.fasta query.fasta
ragtag.py scaffold -o out_2 ref2.fasta query.fasta
ragtag.py merge query.fasta out_*/*.agp

# use Hi-C to resolve conflicts
ragtag.py merge -b hic.bam query.fasta out_*/*.agp

Docs

Please see the Wiki for detailed documentation.

Dependencies

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

Citation

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

Acknowledgments

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. RagTag "merge" was inspired by CAMSA. The developer of CAMSA, Sergey Aganezov, helped review relevant RagTag code.