RolyPoly-tk Data Bundle: reference profiles and sequence sets for virus analyses

RolyPoly data bundle Date / Bundle Version: 2026-10-26 This deposit contains the custom built and reference (3rd party) data required for all functionality of RolyPoly-tk, an RNA-Virus analysis tool kit. This includes external raw databases, bundled for convinenve, and custom, purpose built datasets only released and tracked here. Note that some of the public databases bundled have been processed and differ from the original (e.g. NCBI ribovirus sequences were masked for low complexity regions). Included here are the HMMer/mmseqs/cmscan profile collections, and all the various supporting sequence sets (rRNA collection, taxonomy mapping, adapter sequences, viral proteins with known functions) used by different commands - the marker protein and nucleic similarity based searches, raw NGS read filtering and processing, and genome annotation. Some of the buncdled datasets (e.g. the mitochodria, plastid, and tRNA sequence collections) are not currently exposed by rolypoly-tk codebase, and are should be treated as auxiliary collections prepared for experimental or future use. N.B. if you use any of the external or 3rd party datasets from this bundle, please cite them directly (bibliography details below). Code Compatibility: v0.8.1 Directory tree data/ ├── README.md ├── contam/ │ ├── adapters/ # adapter sequences used during read filtering │ ├── masking/ # viral nucleotide/protein masking references │ └── rrna/ # SILVA/NCBI rRNA masking references and mapping table ├── profiles/ │ ├── cm/ # pressed Rfam covariance-model database │ ├── hmmdbs/ # HMMER DBs, including split RVMT RdRp/RT profiles │ ├── mmseqs_dbs/ # matching MMseqs2 profile databases │ ├── genomad_rna_viral_markers_with_annotation.csv.gz │ ├── marker_features.tsv.gz │ ├── motif_metadata.json │ ├── NVPC_descriptions.csv.gz │ ├── pfam_rdrps_and_rts_profiles.tsv.gz │ ├── rfam_family.tsv.gz │ ├── rfam_family.tsv.build.json │ ├── rvmt_motif_profiles.tsv.gz │ └── vfam.annotations.tsv.gz ├── reference_seqs/ │ ├── ncbi_virus/ # NCBI virus taxonomy DBs and RefSeq viral nucleotide DBs │ ├── RVMT/ # cleaned RVMT sequence DBs │ └── uniref/ # viral UniRef50 subset └── rrna/ # selected rRNA covariance models and cmscan audit tables Changes in this version (2026-10-26) The Pfam RdRp/RT companion set (HMMER, MMseqs2 and pfam_rdrps_and_rts_profiles.tsv.gz) grows from 13 to 16 profiles, adding Arena_RNA_pol (PF06317.17), Flu_PB1 (PF00602.23) and Mononeg_RNA_pol (PF00946.25), selected from the pinned Pfam 38.2 HMM and seed. marker_features.tsv.gz grows from 1,344 to 1,375 labelled-feature rows. The 1,344 existing RVMT rows are unchanged. Added: 13 direct and 14 propagated structure-derived rows for negative-strand RVMT profiles (motif C GDN/GDNQ/SDD; for Peribunyaviridae also motifs A-F and optional H; optional fingers regions for Mononegavirales/Rhabdoviridae), and four rows for Arena_RNA_pol and Flu_PB1 (motif C SDD and a single-Asp motif A). A single-Asp motif A does not meet the positive-strand D-x(4,5)-D pattern and is labelled as such. Labels mark catalytic residue positions and are not validated motif extents. The annotated RVMT Stockholm alignments no longer write multi-character labels into feature tracks (five invalid tracks fixed). Added profiles/rfam_family.tsv.gz and its provenance file rfam_family.tsv.build.json: Rfam 15.1 family metadata (accession, curated type, description), used by annotate-rna to assign Sequence Ontology feature types. Disclaimer Parts of this data archive were prepared from publicly available biological databases and reference resources. Before inclusion in RolyPoly, some of these resources were filtered, deduplicated, masked, compressed, converted into the formats required by and compatible with RolyPoly, or enriched with metadata and annotations. In some cases, only selected subsets or curated profiles were retained. It is uploaded here for versioning, sharing, and disclousre, and I can not vouch for using these data outside of rolypoly. We take and hold no responsibility for any outcome of any usage of this archive. Attribution note This archive includes third-party databases and derived products. We do not own these resources and we do not take responsibility for their completeness, accuracy, licensing, or any downstream use. Please respect the original licenses and data-use terms of the underlying sources. When using this archive, users should cite: RolyPoly itself The specific original third-party database(s) used for the relevant data subset Any software tools used to generate, index, or process the data, where applicable Note: rolypoly-tk commands and log files have a citation-reminder feature, that will try to provide you with the exact 3rd party tools and dbs used by the specific command you used. This can be turned on by changing the rpconfig.json file (see configuration). Third-party databases and citations Please cite the relevant original databases and software alongside RolyPoly when using these resources.A complete list of DOIs related to tools and databases is available in all_used_tools_dbs_citations.json Core reference databases RVMT Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I.-M., Ivanova, N., Zeigler Allen, L., Paez-Espino, D., Bryant, D. A., Bhaya, D., Narrowe, A. B., Probst, A. J., Sczyrba, A., Kohler, A., Séguin, A., Shade, A., Campbell, B. J., Lindahl, B. D., Reese, B. K., Roque, B. M., DeRito, C., Averill, C., Cullen, D., Beck, D. A. C., Walsh, D. A., Ward, D. M., Wu, D., Eloe-Fadrosh, E., Brodie, E. L., Young, E. B., Lilleskov, E. A., Castillo, F. J., Martin, F. M., LeCleir, G. R., Attwood, G. T., Cadillo-Quiroz, H., Simon, H. M., Hewson, I., Grigoriev, I. V., Tiedje, J. M., Jansson, J. K., Lee, J., VanderGheynst, J. S., Dangl, J., Bowman, J. S., Blanchard, J. L., Bowen, J. L., Xu, J., Banfield, J. F., Deming, J. W., Kostka, J. E., Gladden, J. M., Rapp, J. Z., Sharpe, J., McMahon, K. D., Treseder, K. K., Bidle, K. D., Wrighton, K. C., Thamatrakoln, K., Nüsslein, K., Meredith, L. K., Ramirez, L., Buee, M., Huntemann, M., Kalyuzhnaya, M., Waldrop, M. P., Sullivan, M. B., Schrenk, M. O., Hess, M., Vega, M. A., O’Malley, M. A., Medina, M., Gilbert, N. E., Delherbe, N., Mason, O. U., Dijkstra, P., Chuckran, P. F., Baldrian, P., Constant, P., Stepanauskas, R., Daly, R. A., Lamendella, R., Gruninger, R. J., McKay, R. M., Hylander, S., Lebeis, S. L., Esser, S. P., Acinas, S. G., Wilhelm, S. S., Singer, S. W., Tringe, S. S., Woyke, T., Reddy, T. B. K., Bell, T. H., Mock, T., McAllister, T., Thiel, V., Denef, V. J., Liu, W.-T., Martens-Habbena, W., Allen Liu, X.-J., Cooper, Z. S., Wang, Z., Krupovic, M., Dolja, V. V., Kyrpides, N. C., and Koonin, E. V. (2022). The global virome of the ocean. Cell, 185(16), 2879–2894. https://doi.org/10.1016/j.cell.2022.08.023 Rfam Kalvari, I., Nawrocki, E. P., Ontiveros-Palacios, N., Argasinska, J., Lamkiewicz, K., Marz, M., Griffiths-Jones, S., Toffano-Nioche, C., Gautheret, D., Weinberg, Z., Rivas, E., Eddy, S. R., Finn, R. D., and Bateman, A. (2020). Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Research, 49(D1), D192–D200. https://doi.org/10.1093/nar/gkaa1047 RefSeq O’Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., Astashyn, A., Badretdin, A., Bao, Y., Blinkova, O., Brover, V., Chetvernin, V., Choi, J., Cox, E., Ermolaeva, O., Farrell, C. M., Goldfarb, T., Gupta, T., Haft, D., Hatcher, E., Hlavina, W., Joardar, V. S., Kodali, V. K., Li, W., Maglott, D., Masterson, P., McGarvey, K. M., Murphy, M. R., O’Neill, K., Pujar, S., Rangwala, S. H., Rausch, D., Riddick, L. D., Schoch, C., Shkeda, A., Storz, S. S., Sun, H., Thibaud-Nissen, F., Tolstoy, I., Tully, R. E., Vatsan, A. R., Wallin, C., Webb, D., Wu, W., Landrum, M. J., Kimchi, A., Tatusova, T., and DiCuccio, M. (2015). Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1), D733–D745. https://doi.org/10.1093%2Fnar%2Fgkv1189 SILVA Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F. O. (2012). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596. https://doi.org/10.1093/nar/gks1219 UniRef50 UniProt Consortium. UniProt Reference Clusters (UniRef). https://www.uniprot.org/help/uniref Profile and marker databases geNomad RNA viral markers Camargo, A. P., Roux, S., and others. geNomad: identification of mobile genetic elements and viruses from metagenomes. Nature Biotechnology, 2024. https://doi.org/10.1038/s41587-023-01953-y RdRp-Scan Charon, J., Buchmann, J. P., Sadiq, S., and Holmes, E. C. (2022). RdRp-scan: a bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Virus Evolution, 8(2). https://doi.org/10.1093/ve/veac082 NeoRdRp v2.1 Sakaguchi, S., Urayama, S., Takaki, Y., Hirosuna, K., Wu, H., Suzuki, Y., Nunoura, T., Nakano, T., Nakagawa, S., and others. (2022). NeoRdRp: a comprehensive dataset for identifying RNA-dependent RNA polymerases of various RNA viruses from metatranscriptomic data. Microbes and Environments, 37(3). https://doi.org/10.1264/jsme2.ME22001 Pfam Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., and Bateman, A. (2020). Pfam: The protein families database in 2021. Nucleic Acids Research, 49(D1), D412–D419. https://doi.org/10.1093/nar/gkaa913 Structure-derived motif annotations (RdRp motifs A and C) Motif labels for negative-strand polymerases were anchored on published structures and checked against PROSITE profiles PS50507, PS50525 and PS50526 (PDOC50507; used as a labelling source only, no PROSITE profile or alignment is included in this bundle) and UniProt sequences. Structures: LACV L (PDB 5AMR, 10.1016/j.cell.2015.05.006), VSV L (5A22, 10.1016/j.cell.2015.06.018), influenza A polymerase (6QNW, 10.1038/s41586-019-1530-7), Machupo L (7VGQ, 10.1038/s41467-021-26432-3), LCMV L (7X6S, 10.1093/procel/pwad018). VFam / VOGDB The VOGDB / VFam resource. See the original VOGDB/VFam publications and associated database pages for citation details. https://doi.org/10.3390/v16081191 Software used to generate or index the data These tools were used in preparing the archive and should be cited where relevant: HMMER Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS Computational Biology, 7(10), e1002195. https://doi.org/10.1371/journal.pcbi.1002195 MMseqs2 Steinegger, M. and Söding, J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 35(11), 1026–1028. https://doi.org/10.1038/nbt.3988 Infernal / cmsearch Nawrocki, E. P. and Eddy, S. R. (2013). Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29(22), 2933–2942. https://doi.org/10.1093/bioinformatics/btt509 seqkit Shen, W., Sipos, B., and Zhao, L. (2024). SeqKit2: a Swiss army knife for sequence and alignment processing. iMeta, 3(3). https://doi.org/10.1002/imt2.191 BBMap Bushnell, B., Rood, J., and Singer, E. (2017). BBMerge – accurate paired shotgun read merging via overlap. PLOS ONE, 12(10), e0185056. https://doi.org/10.1371/journal.pone.0185056 tRNAscan-SE Lowe, T. M. and Eddy, S. R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5), 955–964. https://doi.org/10.1093/nar/25.5.955 ARAGORN Laslett, D. and Canback, B. (2004). ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research, 32(1), 11–16. https://doi.org/10.1093/nar/gkh152 RolyPoly's actual citation RolyPoly is still under active development, so when using this data bundle in a publication or report, please cite the Zenodo deposit DOI, the RolyPoly GitHub repository, and the exact software/data versions you used. Please also cite the underlying third-party databases and tools that were used for the particular subsets you accessed. Neri, U., Karapliafis, D., De Coninck, L., Camargo, A. P., Bushnell, B., Schulz, F., Steindorff, A. S., Coclet, C., Parker, D., Roux, S. and others, (2026). RolyPoly: a pipeline for RNA virus identification from RNA-seq data. [Software]. Available from https://github.com/UriNeri/rolypoly. (this) Data bundle DOI: 10.5281/zenodo.22636256 Data collection generation and reproducibilty This data collection is generated by periodic (but not scheduled or routine) execution of several scripts. The most relevant files detailing this process are in the rolypoly-db github repository. Other relvent files or historical build details may be in: data/README (here, bundled): detailed description of the bundle layout, preparation dates, and the main data sets included in the archive. This includes the versions of the bundled data, and key changes between teh bundle versions. Software CHANGELOG: version history, including changes to the data bundle and compatibility notes for each release. src/rolypoly/commands/misc/get_external_data.py: the downloader used by the rolypoly get-data workflow; this is what fetches and extracts the packaged data tarball into the configured data directory. src/rolypoly/utils/logging/all_used_tools_dbs_citations.json: the canonical citation mapping used by RolyPoly for tools and databases. The Json fields include the DOI and internal naming of the tool/database.