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RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

• Homology-based misassemblycorrection
• Homology-based assemblyscaffolding andpatching
• Scaffoldmerging

RagTag also providescommand line utilities for working with common genome assembly file formats.

# install with condaconda install -c bioconda ragtag# correct a query assemblyragtag.py correct ref.fasta query.fasta# scaffold a query assemblyragtag.py scaffold ref.fasta query.fasta# scaffold with multiple references/mapsragtag.py scaffold -o out_1 ref1.fasta query.fastaragtag.py scaffold -o out_2 ref2.fasta query.fastaragtag.py merge query.fasta out_*/*.agp other.map.agp# use Hi-C to resolve conflictsragtag.py merge -b hic.bam query.fasta out_*/*.agp other.map.agp# make joins and fill gaps in target.fa using sequences from query.faragtag.py patch target.fa query.fa

Please see theWiki for detailed documentation.

• Minimap2,Unimap, orNucmer
• Python 3 (with the following auto-installed packages)
  • numpy
  • intervaltree
  • pysam
  • networkx

• Alonge, Michael, et al."Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing." Genome Biology (2022).
  https://doi.org/10.1186/s13059-022-02823-7

RagTag supersedes RaGOO:

• Alonge, Michael, et al."RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17.
  https://doi.org/10.1186/s13059-019-1829-6

Many of the major algorithmic improvements relative to RaGOO's first release were provided by Aleksey Zimin, lead developer of theMaSuRCA assembler.Luca Venturini suggested and initially implemented many feature enhancements, such as pysam integration. RagTag "merge" was inspired byCAMSA. The developer of CAMSA,Sergey Aganezov, helped review relevant RagTag code. RagTag "patch" was inspired byGrafter, a scaffolding tool written byMelanie Kirsche. Melanie provided guidance for the RagTag implementation.Michael Schatz has provided guidance for the whole project.