PHORAGER - HumGut database genomes without prophages

Résumé fourni par la source

Prophage-depleted HumGut representative genomes ("phoraged" genomes) This archive contains prophage-depleted bacterial genomes derived from the HumGut collection of human gut prokaryotic genomes. Each genome is a HumGut cluster representative from which predicted prophage regions have been removed ("excised") using the PHORAGER pipeline. The resulting genomes are intended as prophage-depleted host references; for example, for building mock-community references and benchmarking prophage-detection methods. - Pipeline: PHORAGER v0.5.0-beta : https://github.com/aponsero/PHORAGER- Generated by: the PHORAGER `prophage` workflows, run with default parameters.- Humgut database available at: http://arken.nmbu.no/~larssn/humgut/- HumGut database described in : https://doi.org/10.1186/s40168-021-01114-w--> Number of genomes: 30,691 HumGut cluster representatives --- 1. What is in this archive This archive provides one gzipped FASTA per genome plus a single summary table. Item Type Content _phoraged.fasta.gz gzipped FASTA (nt) One HumGut representative genome after prophage excision (host sequence only). humgut_summary.tsv TSV Per-genome taxonomy and prophage-excision summary (one row per genome). Upload structure: To keep individual uploads manageable, the genomes are split into batches of 5,000 and distributed as separate ZIP files, named by genome range : `Humgut1_5000`, `Humgut5000_10000`, `Humgut10000_15000`, and so on. With 30,691 genomes this gives seven ZIP files, the last of which is smaller than 5,000. File naming: Each genome file is named ` _phoraged.fasta.gz`, where ` ` is the HumGut cluster representative identifier (e.g. `HumGut_17012`). This identifier is the join key to `humgut_summary.tsv` (`HumGut_name` column). ------------------------------------------------------------------------------------------------------------------------------------------------ 2. File descriptions 2.1 ` _phoraged.fasta.gz` : prophage-depleted genome Nucleotide FASTA (gzip-compressed) containing the retained host sequence of a single HumGut representative genome after prophage excision. Contigs that contained no predicted prophage are included unchanged; contigs that contained an internal prophage are split into their host flank(s); contigs predicted to be entirely prophage are omitted (see §3). Contig headers take one of two forms: - Unmodified contigs (no prophage removed) retain their original renamed contig header.- Host fragments produced by splitting a prophage-containing contig carry a coordinate suffix indicating the retained interval, `..._host_ _ ` (1-based, inclusive, relative to the pre-excision contig). 2.2 `humgut_summary.tsv` — per-genome taxonomy and excision summary Tab-separated, one row per genome. Column Description `HumGut_name` HumGut cluster representative identifier; matches the ` ` prefix of the corresponding `_phoraged.fasta.gz` file. `HumGut_tax_id` HumGut taxonomy identifier for the cluster. `gtdbtk_taxonomy` GTDB-based taxonomic assignment (domain → species), semicolon-delimited. `original_genome_file` Filename of the original (pre-excision) genome assembly used as input to PHORAGER. `n_prophage_regions` Number of prophage regions excised from this genome. `0` if no prophage was detected. `total_prophage_bp` Total length (bp) of sequence removed as prophage. `0` if none. ------------------------------------------------------------------------------------------------------------------------------------------------ 3. How prophages were excised Excision was performed in two stages: prophage prediction with PHORAGER, followed by removal of the predicted regions from each genome. Prediction. Each genome's contigs were renamed to unique identifiers and screened for prophages with geNomad and VIBRANT. Overlapping predictions from the two tools were consolidated into non-redundant coordinate ranges per contig (1-based, inclusive). Excision. For each contig: - Contigs with no predicted prophage were retained unchanged.- Contigs containing an internal prophage (host sequence remaining on at least one side) had the prophage region(s) removed and the flanking host sequence retained. Such a contig is split into separate host fragments rather than rejoined, so no artificial host–host junction is created.- Contigs predicted to be entirely prophage: whole-contig predictions, or predictions spanning the full contig length were removed in their entirety.- Host fragments were kept regardless of length (no minimum-length filter was applied). Only retained host sequence is included in this archive. Detection-stage regions are not annotation-confirmed. The regions removed here are PHORAGER's consolidated geNomad/VIBRANT predictions. They were deliberately NOT passed through PHORAGER's downstream confirmation steps (CheckV quality assessment and Pharokka/Phold annotation-based filtering). This is the conservative choice for building prophage-depleted host genomes: any region flagged by either detection tool is removed, minimizing the chance that a genuine prophage remains in a genome presented as host, at the cost of occasionally removing sequence that later confirmation might have retained. Consequently: - The excised prophage sequences are NOT distributed in this archive and should not be treated as a validated prophage set.- `n_prophage_regions` and `total_prophage_bp` describe the detection-stage sequence that was removed; they are not a confirmed prophage count. ------------------------------------------------------------------------------------------------------------------------------------------------ 4. Notes and limitations - Region boundaries are as predicted by geNomad/VIBRANT and are not CheckV-trimmed. A small amount of host sequence may be removed at region edges, and conversely some prophage-adjacent bases may remain in the host output.- `n_prophage_regions = 0` means no prophage was detected for that genome; it is not a guarantee that the genome is prophage-free.- Genomes are provided as prophage-depleted contig sets. Contigs carrying internal prophages are split and are not re-scaffolded or otherwise re-assembled. ------------------------------------------------------------------------------------------------------------------------------------------------ 5. How these outputs were generated Provenance chain: HumGut representative genome → PHORAGER prophage detection (geNomad + VIBRANT, consolidated) → prophage excision (this archive: host sequence retained) Tool versions: Tool Version Role PHORAGER v0.5.0 Pipeline (detection + excision) geNomad 1.8.1 Prophage prediction VIBRANT 1.2.1 Prophage prediction Parameters : PHORAGER prophage subworkflow using default parameters

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.