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Software nameMTB-Explorer SoftwareDeeplex® Myc-TBMycobacterium tuberculosis
WGS data analysis platform		CLC Genomics WB Premium Network
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CompanyMGIGenoScreen(illumina Partner)Uni-medica(深圳联合医学科技有限公司) QIAGEN
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Introduction1.WGS and ATOPlex targeted deep sequencing data can be analyzed
2. One-click operation
3. English and Chinese interface
4. Identification of mixed infection can be performed		The automated data analysis via the Deeplex® Myc-TB secure web application for targeted deep sequencing
1. Directly applicable to clinical samples.
2. Prediction of resistance to 15 anti-TB drugs.
3. Predict >97%** of MTBC resistance profiles detected by whole genome sequencing, identify heteroresistance down to 3% subpopulations and work with DNA loads down to 100 genomes.
4. Identification of more than 140 mycobacterial species,including most species of clinical or veterinary relevance: MTBC, M. kansasii, M. abscessus, M. intracellulare, M. avium complex, and many more. Detect co-infection/co-colonization with distinct species.
The platform can automatically perform variant detection in Mycobacterium tuberculosis whole genome sequencing data, including quality control, mapping, and variant annotation, with a friendly interface and simple operation.Only suitable for WGS data analysis
1. A variety of CLC software functions - metagenomic, amplicon and WGS data can be analyzed
2. Pure software, flexible installation and charging
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Functionquality screening of sequencing data, genome mapping, mutation and drug resistance detection, lineage, spoligotype, and phylogenetic treeIdentification of more than 140 mycobacterial species, MTBC genotyping and spoligotyping, Prediction of resistance to 15 anti-TB drugsThe platform can predict resistance to 17 commonly used anti-tuberculosis drugs and sensitivity to the four firstline drugs for a sample.
In addition to the multiple analysis functions, such as drug resistance prediction, species/subtype identification, phylogenetic tree construction, and pairwise SNP distance analysis, the platform also has data storage and sample management functions.		Sequence quality control, alignment (reference genome H37Rv), variation detection (SNP, InDels, SV), realignment, evolutionary traceability, low frequency mutation detection, drug resistance database comparison, output of variation, gene and drug resistance results, explore the influence of variation on drug target interactions in a three-dimensional protein model
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OutputSingle sample report and multiple phylogenetic tree construction resultsOne report per sample, easy to querySingle sample variation detection, SNP distance between strains, phylogenetic tree construction each function outputs a webpage report contentNo report. Results are in the intermediate directory
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DataBaseDetection of 15 drug resistance of the WHO list.
MTB identification：Nucleotide homology of hsp65 gene.
spoligotype.		①Drug resistance gene test: The assay can predict resistance to 15 anti-tuberculosis drugs including the more recently introduced compounds such as bedaquiline and linezolid,from 18 main MTBC gene targets associated with resistance to first an second line drugs .②MTB identification: nucleotide homology of the hsp65 gene
③spoligotyping: MTBC strains are spoligotyped by detecting the presence-absence pattern of 43 spacers in the CRISPR locus.		The platform can predict resistance to 17 commonly used anti-tuberculosis drugs and sensitivity to the four firstline drugs for a sample, providing a reference for clinical medication.The platform can analyze genetic distances between strains.Data from published articles are used for the drug resistance database, and also supports user-defined database upload
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Limitations WGS can currently only be performed reliably and cost-effectively using culture isolates, due to the need for large amounts of good quality DNA.It can only be analyzed on a web page and cannot be installed on a serverIt can only be analyzed on the web, not localized1. Pure English interface
2. There are more modules, and it is convenient to use multiple modules in series
3. There is no TB specific drug resistance database
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Time(h)16 sample/h,（5M PE reads/sample）1h Deeplex web appNANA
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PriceThe charge is included with the kitThere is no charge for the services provided by the SAM-TB platform. Registered users will be provided with the storage and computing resources required to analyze 100 samples. If more samples need to be analyzed, please contact the platform for review.56,863 CNY/year
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Web site/https://www.deeplex.com/https://samtb.uni-medica.com/indexhttp://www.clcbio.com
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