see https://github.com/downingtim/LSDV-PVG for the latest version
This was the code and data repository for the lumpy skin disease virus (LSDV) pangenome variation graph (PVG).
The foler 121_SAMPLE_PVG contains data for the PVG created from all available valid LSDV genomes (n=121).
1.1 For these samples, the download process takes us through file download from NCBI Nucleotide, metadata extraction, symbol removal, an initial phylogeny, a genome length check, reporting of excluded sequences, and a final output FASTA.
1.2 We take the above fasta and use PGGB to construct a PVG from it.
1.3 odgi etc
The foler 6_SAMPLE_PVG contains data for the PVG created from 6 representative LSDV genomes for computationally efficient investigation.
2.1 PGGB etc
This folder contains tests run of the nf-core pangenome tool for LSDV, GPV, SPV and CaPV.
Tim Downing, Chandana Tennakoon, Thibaut Freville