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.

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.

Databases

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.

Used in the study:
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

MyCodentifier Github:

https://jordycoolen.github.io/MyCodentifier/