Databases for MyCodentifier: A tool for routine identification of nontuberculous mycobacteria using MGIT enriched shotgun metagenomics.
Authors/Creators
- 1. Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- 2. Radboudumc Center for Infectious Diseases, Department of pulmonary diseases, Radboud University Medical Center, Nijmegen, the Netherlands
Description
Databases used for MyCodentifier a Nextflow pipeline to identify Mycobacterium tuberculosis complex (MTBC) and Nontuberculous mycobacteria (NTM) species from Next-generation sequencing (NGS) data.
Short description:
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.
| Name | Short Description |
| 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 et al 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 et al 2017 Mycobacterium strains. |
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Used in the study: |
Databases available via ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data or https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database |
MyCodentifier Github:
https://jordycoolen.github.io/MyCodentifier/