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