Data from Matrishin et al. "Pervasive integrative and conjugative elements shape Porphyromonas gingivalis gene repertoires"

Data files associated with Matrishin et al. "Pervasive integrative and conjugative elements shape Porphyromonas gingivalis gene repertoires". Directory or File Contents 01.Pg_Bakta_gbffs Bakta GenBank format files for the 36 Pg genomes with complete assemblies (in "complete_genomes" subfolder) and 63 Pg genomes that required scaffolding (in "scaffolded_genomes" subfolder). 02.PgICE_cores_fastas Nucleotide fasta files for the 160 extracted ICE conjugation module regions ("cores"). 03.curated_PgICE_fastas Nucleotide fasta files for the curated and extracted ICEs in Pg_ICE_pilot_set_111. 04.curated_PgICE_gffs gff files for the curated and extracted ICEs in Pg_ICE_pilot_set_111, including Bakta annotations. 05.curated_PgICE_gbs GenBank format files for the curated and extracted ICEs in Pg_ICE_pilot_set_111, including Bakta annotations. 06.PgICE_G1_G2_pangenomes PPanGGOLiN analysis output files for all ICE 111 ICEs together (Pg_ICE_pilot_set_111_ppanggolin.zip; to define common set of gene families across all ICEs), and output files for separate pangenome analyses for each of Group 1 and Group 2 ICEs in Pg_ICE_pilot_set_89 (Pg_ICE_pilot_set_90.subset_89.Group_1.MMSEQS.zip, Pg_ICE_pilot_set_90.subset_89.Group_2.MMSEQS.zip); note that references to "Pg_ICE_pilot_set_90.subset_89" reflect nomenclature at runtime, subsequently condensed to "Pg_ICE_pilot_set_89"