Fast reference-guided genome assembly scaffolding
Project description
RagTag
Reference-guided genome assembly correction and scaffolding. RagTag is the successor to RaGOO.
Getting Started
git clone https://github.com/malonge/RagTag
cd RagTag
python3 setup.py install
# correct contigs
ragtag.py correct ref.fasta query.fasta
# scaffold contigs
ragtag.py scaffold ref.fa ragtag_output/query.corrected.fasta
Dependencies
Citation
Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17.
Acknowledgments
Many of the major algorithmic improvements relative to RaGOO's first release were provided by Aleksey Zimin, lead developer of the MaSuRCA assembler. This includes the use of read-mapping for misassembly validation as well as the use of alignment merging for improved scaffolding. Luca Venturini also suggested and initially implemented many feature enhancments, such as pysam integration.
*More Docs Soon*
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