This is a Bowtie2 index built using full NCBI non-redundant NT / NR records from January 2021 that includes all microbial, verterbrate, non-verterbrate and plant organisms. The index was built by Nikolay Oskolkov, Lund University, Sweden, within the NBIS SciLifeLab long-term support project, PI Anders Götherström, Centre for Palaeogenetics, Stockholm, Sweden. The index was build using Bowtie2 version 2.3.5.1 using a computer node with 1 TB of RAM on Uppmax SUPR /SNIC HPC cluster. Questions regarding the index should be sent to nikolay.oskolkov@scilifelab.se The index was built using the command lines below: bowtie2-build --large-index library.fna library.fna --threads 20 DOI: 10.17044/scilifelab.21070063 When using this Bowtie2 index for your research please cite our preprint: https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1