Some Resources dedicated to Mycobacterium tuberculosis complex (MTBCtools)

Biological databases

CPLP-TB (link to publication) main goal is to facilitate exchange of molecular epidemiological data and thus enable the tracking of important MTB clones across the Lusophone space

GMTV (link to publication) integrates clinical, epidemiological and microbiological description with genome variations based on WGS data

inTB (link to publication) is a web-based system for storage and analysis of clinical, socio-demographic and molecular typing data

Mbovis.org (link to publication) hosts the Mycobacterium bovis Spoligotype Database

MtbRegList (link to publication) is a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis

Mycobrowser (link to publication) is a comprehensive genomic and proteomic data repository for pathogenic mycobacteria

MycoDB.es (link to publication) is the Spanish Database of Animal Mycobacterosis

MIRU-VNTRplus (link to publication) is a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria

ReSeqTB (link to publication) is a collaborative effort for a centralized worldwide TB relational sequencing data platform

SpolDB4 (link to publication) is the the fourth international spoligotyping database for MTBC classification, population genetics and epidemiology

SITVITWEB (link to publication) is the fifth international multimarker database for studying MTBC genetic diversity and molecular epidemiology

SITVIT2 (link to publication) is the sixth international multimarker database for studying MTBC genetic diversity and molecular epidemiology

tbvar (link to publication) is the Mycobacterium tuberculosis variome resource

TB database (link to publication) is an integrated platform for tuberculosis research

TB Portals (link to publication) is an open-access, web-based platform for global drug-resistant-tuberculosis data sharing and analysis

TB DEPOT (link to publication) is a multi-domain tuberculosis data analysis resource

Prediction/classification tools

CASTB (link to publication) is a total solution for epidemiological and genomic analysis of Mycobacterium tuberculosis complex

COMBAT-TB-NeoDB (link to publication) is a comprehensive bacterial analytical toolkit for TB Research (and related projects)

CRISPRbuilder-TB (link to publication) reconstructs the whole CRISPR locus from a Mycobacterium tuberculosis complex genome, by using SRA WGS data

Galru (link to publication) identifies Mycobacterium tuberculosis spoligotyping from uncorrected long reads

KvarQ (link to publication) performs targeted and direct variant calling in FastQ reads of bacterial genomes

MIRU-profiler (link to publication) performs digital 24-loci MIRU-VNTR typing for Mycobacterium tuberculosis

MIRUReader (link to publication) identifies 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex directly from long reads

MixInfect (link to publication) detects mixed infections in TB

MTBseq (link to publication) is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from WGS TB data

PhyTB (link to publication) is a web-tool to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism

PolyTB (link to publication) is a genomic variation map for Mycobacterium tuberculosis

SecProMTB (link to publication) is a Support Vector Machine-Based classifier for secretory proteins using imbalanced data sets applied to Mycobacterium tuberculosis

SNP-IT (link to publication) is a Whole-genome SNP based identification tool for members of the Mycobacterium tuberculosis complex

StackTB (link to publication) is a package for classifying the lineage of Mycobacterium tuberculosis strains from MIRU-VNTR data

SpolLineages (link to publication) predicts Mycobacterium tuberculosis complex spoligotype families

SpolPred (link to publication) predicts Mycobacterium tuberculosis spoligotypes from short genomic sequences

SpolSimilaritySearch (link to publication) is a web tool allowing to search for similar spoligotyping profiles in function of a given query

SpolTools (link to publication) are online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex

SpoTyping (link to publication) provides fast and accurate in silico Mycobacterium spoligotyping from sequence reads

TB-Lineage (link to publication) determines the major genetic lineage of a Mycobacterium tuberculosis isolate through various methods

TBminer (link to publication) predicts MTBC lineages from spoligotypes and MIRU-VNTR profiles basing on Machine Learning

TGS-TB (link to publication) provides total genotyping solution for MTB using short-read Whole Genome Sequencing

UVP (link to publication) is a unified analysis variant pipeline to identify variants and assign lineage from MTBC sequence data

Drug resistance

binoSNP (link to publication) detects low-frequency SNPs in NGS data of Mycobacterium tuberculosis complex strains

DeepAMR (link to publication) predicts co-occurrent resistance of Mycobacterium tuberculosis

MUBII-TB-DB (link to publication) is a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis

Mykrobe predictor (link to publication) predicts antibiotic-resistance from genome sequence data for S. aureus and M. tuberculosis

PhyResSE (link to publication) is a a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from WGS data

Resistance Sniffer (link to publication) predicts drug resistance in Mtb isolates using complete or partial genome datasets in different file formats

TBDReaMDB (link to publication) is a comprehensive database listing mutations associated with TB drug resistance

TBProfiler (link to publication) is a pipeline allowing to analyse M. tuberculosis WGS data to predict lineage and drug resistance

Other web portals

WHO provides global report and other important information on TB

E-DETECT TB (link to publication) is a research consortium for the early detection and integrated management of TB in Europe

The Union works towards the global elimination of TB

CDC provides TB reports and data for the United States of America

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