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Usage
Michael Alonge edited this page Nov 1, 2021
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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.
Are these docs confusing or incomplete? Please open an issue and let me know.