Bowtie2 index for pathogenic microbial species of NCBI NT from May 2020

This is a Bowtie2 index built using a subset of NCBI non-redundant NT / NR records from May 2020, https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz, that includes only microbial pathogenic organisms. The Bowtie2 index was built using a custom very permissive list (e.g. opportunistic pathogens were included) pathogensFound.very_inclusive.tab of pathogenic microbes based on extensive literature search. The Bowtie2 index can be used in metagenomic projects for alignment against pathogenic references and detecting pathogenic organisms present in metagenomic samples. 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.