RagTag 2.1.0

RagTag

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.

Location and version:

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$ which ragtag.py
/local/cluster/bin/ragtag.py
$ ragtag.py --version
v2.1.0

help message:

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$ ragtag.py --help

RagTag: Tools for fast and flexible genome assembly scaffolding and improvement.
Version: v2.1.0

usage: ragtag.py <command> [options]

    assembly improvement:
      correct         homology-based misassembly correction
      scaffold        homology-based assembly scaffolding
      patch           homology-based assembly patching
      merge           scaffold merging

    file utilities:
      agp2fa          build a FASTA file from an AGP file
      agpcheck        check for valid AGP file format
      asmstats        assembly statistics
      splitasm        split an assembly at gaps
      delta2paf       delta to PAF file conversion
      paf2delta       PAF to delta file conversion
      updategff       update gff intervals


    options:
      -c, --citation
      -v, --version

software ref: https://github.com/malonge/RagTag
research ref: https://doi.org/10.1101/2021.11.18.469135