biostudies-literatureAllesoe RLMarie Sklodowska-Curie Individual FellowshipNovo Nordisk FoundationMedical Research CouncilNovo Nordisk Foundation Center for Protein ResearchEuropean Union’s Horizon 2020 research and innovation programmeEuropean Union’s Horizon 2020 research and innovation program705-710https://www.ebi.ac.uk/biostudies/studies/S-EPMC8097684biostudies-literatureUnknown37(5)<h4>Summary</h4>Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistanBioinformatics (Oxford, England)Automated download and clean-up of family-specific databases for kmer-based virus identification.PMC8097684NNF14CC0001643476PI Simon Rasmussen874735799417MC_UU_12014/12Koopmans MPGClausen PTLCLemvigh CKCotten MAllesoe RLFlorensa AFPhan MVTLund OfalseAutomated download and clean-up of family-specific databases for kmer-based virus identification.<h4>Summary</h4>Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistan2021-01-01T00:00:00Z2021 May2026-05-08T02:59:17.628Z2022-02-10T09:57:18.722ZS-EPMC80976843303150910.1093/bioinformatics/btaa857