Pangenome Graphs of Bombyx mori BmN4 Cell Genome for 29 Chromosomes

This dataset contains the Bombyx mori BmN4 pangenome graphs for 29 chromosomes. The BmN4 consensus genome and its primary and secondary contigs were partitioned into communities using the partition-before-pggb tool (-n 1 -p 90 -s 5k) included in PGGB (Garrison et al., 2024). For each community, a pangenome graph was constructed using pggb (-s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30 -k 23 -f 0 -B 10M -n 1 -j 0 -e 0 -G 700,1100 -P 1,4,6,2,26,1 -O 0.001 -d 100 -Q Consensus_), with the BmN4 consensus genome as the reference and the Hifiasm.Hybrid primary and secondary contigs as input. The sequences were partitioned into 29 chromosome-corresponding communities, and a separate pangenome graph was generated for each community. The dataset includes: GFA files of the pangenome graphs for each chromosome - One GFA file per chromosome-based community- File naming convention: `BmN4_chr[ID].gfa` (e.g., `BmN4_chr1.gfa`, `BmN4_chr2.gfa`, ..., `BmN4_chrW.gfa`) These resources provide a high-resolution view of structural variation and genome graph topology for the BmN4 genome, and can be used for further comparative genomics and pangenome visualization.