Databases for NEXT-RSV-SEQ (RSV, HMPV, PIV)

Here, we provide databases ready for use in sequencing read decontamination with our Next-RSV-SEQ pipeline (https://gitlab.com/rki_bioinformatics/next-rsv-seq), designed for viral genome assembly using Illumina data.

Available Databases:

Human orthopneumovirus / Human respiratory syncytial virus (RSV): [RSV_GRCh38_2022-04-06.zip]

Human metapneumovirus (HMPV): [HMPV_2022-05-28.zip]

Parainfluenza virus (PIV): [PIV_2022-05-28.zip]

These databases were created using Kraken2 and are based on all complete viral genome sequences available on NCBI Reference Sequence Database (RefSeq) as of April 6, 2022 (for RSV), and May 28, 2022 (for HMPV and PIV). The RSV database also includes the human genome sequence GRCh38 (Genome Reference Consortium Human Build 38). The databases have been compressed into zip format for easy downloading. Before use, please unpack the respective zip archive.