2026-10-08T13:41:19Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34018548 2026-09-28T21:45:24Z category_24208 category_24310 category_24367 item_type_3 month_year_09_2026

RefSeq viral genomes database for mashID - RefSeq release 237 (2026-09-28) Marc-Olivier Duceppe (11048067) Bioinformatics and computational biology not elsewhere classified Genomics Virology mashID Mash MinHash virus viral genomes bacteriophage prophage RefSeq virus identification viral contamination whole genome sequencing sketch database reference database <p dir="ltr">Mash sketch database of all viral genomes in NCBI RefSeq release 237 for virus identification and prophage or viral contamination detection with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- refseq_viral_r237_2026-09-28.msh: Mash 2.3 sketches, k-mer size 21, sketch size 2000, 19,625 RefSeq viral records (complete genomes and genome segments; 6,427 phages), 304 MB. MD5: 7394b54d24840d343ac77e527a53482d</p><p dir="ltr">- refseq_viral_r237_2026-09-28.metadata.tsv: one line per reference with RefSeq accession, organism name (current ICTV species name as recorded by RefSeq), NCBI TaxID, sequence length, sketch hash count, source file and record definition. mashID reads it automatically when it sits next to the .msh file.</p><p dir="ltr">Construction</p><p dir="ltr">The viral division of RefSeq release 237 (viral.1.1.genomic.fna.gz and viral.1.genomic.gbff.gz from ftp.ncbi.nlm.nih.gov/refseq/release/viral) was split into one file per record; organism names and TaxIDs were taken from the GenBank flat file. Every record was sketched with make_mashID_db (sketch size 2000; records shorter than 2000 k-mers keep all their k-mers), with no length filter and no dereplication, since RefSeq holds one reference per virus species or segment. Reproducible with scripts/build_virus_db.sh in the mashID repository.</p><p dir="ltr">Usage</p><p dir="ltr">mashID -i reads/ -o results -d refseq_viral_r237_2026-09-28.msh</p><p dir="ltr">Keep the .metadata.tsv file next to the .msh file. mashID 0.2.9 or later applies no reference-length filter to this database automatically; with older versions add --min-ref-length 0.</p><p dir="ltr">Scope</p><p dir="ltr">Identifies viruses to species against the RefSeq reference and detects complete or partial viral genomes inside other samples, for example prophages in bacterial assemblies. Segmented viruses are represented by their individual segments. Divergent viruses with no close RefSeq relative will not be detected at k=21.</p> 2026-09-28T21:45:24Z Dataset Dataset 10.6084/m9.figshare.34018548.v1 https://figshare.com/articles/dataset/RefSeq_viral_genomes_database_for_mashID_-_RefSeq_release_237_2026-09-28_/34018548 CC BY 4.0