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Fast reference-guided genome assembly scaffolding

Project description




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

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


Getting Started

# install with conda
conda install -c bioconda ragtag

# correct a query assembly correct ref.fasta query.fasta

# scaffold a query assembly scaffold ref.fasta query.fasta

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

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

# make joins and fill gaps in target.fa using sequences from query.fa patch target.fa query.fa


Please see the Wiki for detailed documentation.


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


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. Luca Venturini suggested and initially implemented many feature enhancements, such as pysam integration. RagTag "merge" was inspired by CAMSA. The developer of CAMSA, Sergey Aganezov, helped review relevant RagTag code. RagTag "patch" was inspired by Grafter, a scaffolding tool written by Melanie Kirsche. Melanie provided guidance for the RagTag implementation. Michael Schatz has provided guidance for the whole project.

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