PHORAGER - mining prophages from ESKAPE pathogens

ESKAPE pathogen prophage repertoire : PHORAGER output collection This archive contains the key prophage-mining outputs generated by PHORAGER (Prophage Hunting, vOTU Retrieval, Annotation and Genomic ExploRation) applied to a large collection of publicly available ESKAPE pathogen genomes. - Pipeline: PHORAGER v0.5.0-beta https://github.com/aponsero/PHORAGER- Associated manuscript: Defining the ESKAPE pathogen prophage repertoire with PHORAGER (Dyball et al. bioRXiv)- Generated by: the PHORAGER `bacterial`, `prophage`, `annotation`, and `summarize` workflows, run with default parameters. ------------------------------------------------------------------------------------------------------------------------------------------------ 1. What is in this archive The collection is split into one ZIP file per ESKAPE pathogen. Each ZIP unpacks to a single folder containing five files for that species: File (per species) Type Content PHORAGER stage <Species>_genomes_metadata.tsv TSV NCBI metadata for the input genomes external from NCBI <Species>_bacterial_genome.tsv TSV Per-genome QC metrics + prophage counts `summarize` (bacterial_genome) <Species>_filtered_phage_set.fasta FASTA (nt) Prophage sequences after annotation-based filtering, before dereplication `annotation` (post-filter) <Species>_final_representatives.fasta FASTA (nt) vOTU cluster representative prophages `annotation` (post-clustering) <Species>_prophage_table.tsv TSV Per-prophage table (host, cluster, quality, length, CDS) `summarize` (prophage_table) Species included (six ZIPs): - Enterococcus faecium- Staphylococcus aureus- Klebsiella pneumoniae- Acinetobacter baumannii- Pseudomonas aeruginosa- Enterobacter spp. Folder / file naming. Folders follow `<Species>_<DD.MM.YY>`, where the date is the NCBI download/build date for that species' genome set (these differ between species, e.g. most ESKAPE genomes were retrieved 10 Oct 2025, K. pneumoniae on 22 Oct 2025). Files within a folder are prefixed with the same `<Species>` token. ------------------------------------------------------------------------------------------------------------------------------------------------ 2. File descriptions 2.1 `<Species>_genomes_metadata.tsv` : NCBI input metadata Tab-separated metadata for the bacterial genomes downloaded from NCBI and used as input to PHORAGER. This file is produced by the NCBI download step, not by PHORAGER. 2.2 `<Species>_bacterial_genome.tsv` : per-genome summary One row per genome that passed CheckM2 quality assessment. Columns (exact, as emittedby the pipeline): Column Description Genome_name Genome basename (from CheckM2 `Name`); matches the input genome filename stem (e.g. the NCBI accession) Completeness CheckM2 completeness estimate (%) Contamination CheckM2 contamination estimate (%) Genome_size Total assembly size (bp) GC_content GC fraction Contig_N50 Contig N50 (bp) Coding_sequences Total predicted CDS count Prophage_count Number of prophages attributed to this genome in `filtered_phage_set.fasta` (i.e. the filtered, pre-dereplication set). `0` if none passed filtering > Note: `Prophage_count` is derived from the filtered (non-dereplicated) prophage set,> by attributing each prophage to the genome named before the first `_ctg` in its ID. 2.3 `<Species>_filtered_phage_set.fasta` : filtered prophage sequences Nucleotide FASTA of all prophage sequences that passed PHORAGER's annotation-based filtering, before vOTU dereplication. Each record corresponds to exactly one row in `prophage_table.tsv` (matched on the sequence ID). Sequence-ID format is described in §3. 2.4 `<Species>_final_representatives.fasta` : vOTU representatives Nucleotide FASTA containing one representative sequence per vOTU cluster (95% ANI / 85% aligned fraction by default). These are extracted directly from `filtered_phage_set.fasta`, so every header here also appears in that file and equals a value in the `Cluster_representative` column of `prophage_table.tsv`. Use this file as the non-redundant, species-level prophage set for downstream analysis. 2.5 `<Species>_prophage_table.tsv` : per-prophage summary One row per prophage in `filtered_phage_set.fasta`. Columns (exact, as emitted): Column Description Prophage_name Prophage sequence ID; matches a header in `filtered_phage_set.fasta` Bacterial_host Host genome basename (everything before the first `_ctg` in `Prophage_name`); matches `Genome_name` in the bacterial table. Cluster_representative The vOTU representative for this prophage's cluster. If equal to `Prophage_name`, this prophage is a representative (and appears in `final_representatives.fasta`). `Not_in_clusters` if no cluster assignment was found. CheckV_quality CheckV quality tier (e.g. Complete / High-quality / Medium-quality). `NA` if not found in the CheckV summary. Phage_length Sequence length (bp). Uses CheckV's trimmed `proviral_length` where available, otherwise `contig_length`. CDS_number CDS count from the annotation step. `NA` if detailed annotation was skipped or the prophage was not matched. ------------------------------------------------------------------------------------------------------------------------------------------------ 3. Prophage sequence-naming convention Input contigs are renamed by PHORAGER to `{genome_basename}_ctg{NNN}`, where `genome_basename` is the input genome's filename stem and `NNN` is a zero-padded contig number (3–5 digits, depending on contig count per genome). Prophage records then take one of two forms: - Coordinate-based (merged/consolidated predictions): `{genome_basename}_ctg{NNN}_{start}_{end}` Coordinates are 1-based and inclusive, relative to the renamed contig. Example: `GCF_000123456.1_ctg001_4521_38790`- Whole-contig predictions: `{genome_basename}_ctg{NNN}_complete` Used when a mining tool flagged the entire contig as prophage. CheckV may append a trailing `_1` to trimmed proviral sequences; where present, that suffix is part of the FASTA header and the `Prophage_name` value. ------------------------------------------------------------------------------------------------------------------------------------------------ 4. How the files link together The four PHORAGER files share consistent identifiers, so they can be joined directly: - Prophage → host genome: `prophage_table.Bacterial_host` = `bacterial_genome.Genome_name`.- Prophage row → sequence: `prophage_table.Prophage_name` = FASTA header in `filtered_phage_set.fasta`.- Prophage → its vOTU representative: `prophage_table.Cluster_representative`; the representatives themselves are in `final_representatives.fasta`.- Genome → NCBI metadata: `bacterial_genome.Genome_name` = the accession column in `genomes_metadata.tsv` *(confirm which column — see §2.1)*. ------------------------------------------------------------------------------------------------------------------------------------------------ 5. How these outputs were generated Genomes were processed with PHORAGER v0.5.0-beta using default parameters. In summary(see the associated manuscript for full methods and citations): 1. Bacterial QC & dereplication : CheckM2 quality filtering (default ≥90% completeness, <5% contamination) followed by dRep dereplication at the strain level (default 99.9% ANI).2. Prophage mining & consolidation : geNomad and VIBRANT run in parallel; overlapping predictions consolidated into non-redundant coordinate ranges; sequences extracted.3. Annotation & filtering : CheckV quality assessment; length/quality filtering; annotation with Pharokka (and Phold); structural-gene-based filtering. The `filtered_phage_set.fasta` is the output of this stage.4. vOTU clustering : BLAST + CheckV ANI scripts, clustered at the species level (default 95% ANI / 85% aligned fraction). `final_representatives.fasta` holds the cluster representatives.5. Summaries : `bacterial_genome.tsv` and `prophage_table.tsv`. Tool versions: Tool Version CheckM2 1.0.1 dRep 3.5.0 geNomad 1.8.1 VIBRANT 1.2.1 CheckV 1.0.3 Pharokka 1.9.1 Phold 0.2.0 BLAST+ 2.16.0