downingtim / LSDV_PVG

The lumpy skin disease virus (LSDV) pangenome variation graph (PVG)

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).

1 # The complete LSDV 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

2 # The 6-sample LSDV PVG

The foler 6_SAMPLE_PVG contains data for the PVG created from 6 representative LSDV genomes for computationally efficient investigation.

2.1 PGGB etc

3 # NF_PANGENOME_TEST

This folder contains tests run of the nf-core pangenome tool for LSDV, GPV, SPV and CaPV.

Credits

Tim Downing, Chandana Tennakoon, Thibaut Freville