Databases for MyCodentifier: A tool for routine identification of nontuberculous mycobacteria using MGIT enriched shotgun metagenomics.

Databases used for MyCodentifier a Nextflow pipeline to identify Mycobacterium tuberculosis complex (MTBC) and Nontuberculous mycobacteria (NTM) species from Next-generation sequencing (NGS) data.<br> <br> <strong>Short description:</strong><br> The pipeline is constructed using nextflow as workflow manager running in a docker container. It is able to identify species of MTBC/NTM from positive Mycobacterial Growth Indicator Tube (MGIT) cultures. To do so it uses an hsp65 database for fast identification coupled with a Metagenomic method using centrifuge to identify on genome level. For TB it also is able to identify subspecies. Results are presented in automated pdf and html reports. <strong>Databases</strong> <strong>Name</strong> <strong>Short Description</strong> 20220726_ref.tar.gz 7 major mycobacterial genomes as centrifuge classification database, used for reference-based mapping and genotype resistance prediction 20220726_wgs_centrifuge_db_Radboudumc_MB.tar.gz centrifuge classification database using Tortoli <em>et al</em> 2017 Mycobacterium strains + additional strains genomes.tar.gz 7 major mycobacterial genomes, annotation and Genbank files. Files are paired with 20220726_ref.tar.gz snpEff.tar.gz 7 major mycobacterial genomes annotation models for snpEff. Tortoli_etal_hsp65.tar.gz KMA database of hsp65 gene extractions of the Tortoli <em>et al</em> 2017 Mycobacterium strains. Used in the study:<br> p_compressed+h+v.tar.gz (12/06/2016) Databases available via ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data or https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database <strong>MyCodentifier Github:</strong> https://jordycoolen.github.io/MyCodentifier/