Automated download and clean-up of family-specific databases for kmer-based virus identification.

ABSTRACT:

Summary

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 resistan

SUBMITTER: Allesoe RL 

PROVIDER: S-EPMC8097684 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature