Usage

RagTag Version: v2.1.0

RagTag offers multiple utilities for scaffolding and improving modern genome assemblies. After installing RagTag, use the ragtag.py command to see a list and brief description of these utilities.

RagTag: Tools for fast and flexible genome assembly scaffolding and improvement.
Version: v2.0.1

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

Each utility is invoked with the ragtag.py <command> [options] syntax. Please use the sidebar to navigate to more detailed documentation for each utility.