Data from Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis"

Data files associated with Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis".

Please see the table in 00.README.xlsx for key information regarding nomenclature. We caution that the same locus tag identifiers refer to different genes in the Zenodo files than in NCBI. This difference resulted from use of the same Locus Tag Prefixes for in house gene calls using Bakta for the manuscript analyses as for the PGAP analyses ultimately performed upon submission of the assemblies to GenBank. Unlike the Supplementary Data Files submitted with the manuscript, see below, it was not possible to readily update all the Zenodo-deposited files to their updated final GCA and distinct locus tag identifiers because of the complexity of some of the included filetypes, therefore all files in the Zenodo set were left unchanged from the nomenclature used in the original in house analyses based on Bakta.

Directory
Contents

00.README
Important information regarding nomenclature differences across data types.

01.bax.bakta
Results of Bakta annotation of 88 Pg genomes.

02.bax.ppanggolin
Results of PPanGGOLiN pangenome analysis of 88 Pg genomes.

03.bax.combo
Results of multiple analyses used to inform identification and curation of prophages in Pg genomes, provided as bacterial genome fastas and gff files that can be uploaded together to genome viewer tools (e.g. Geneious) and visualized as tracks. Note, these do not include final prophage calls.

04.phage.genomes
Pg phage genomes in fasta format.

05.phage.prots
Pg phage proteins in fasta format, clipped proteins at the beginnings and ends of genomes are excluded.

06.phage.gbs
Pg phage information in GenBank format, clipped proteins at the beginnings and ends of genomes are excluded.

07.phage.families.virclust
Results of VirClust analysis used to inform resolution family-level units.

08.phage.families.victor
Results of VICTOR analysis used to inform resolution of family-level units.