Clariseq Analytics

Clariseq TB

MTB/NTM Species ID
and Drug Resistance, Simplified.

From raw WGS reads to species identification, lineage and drug-resistance insights — all in one dashboard.

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About ClariSeq TB

ClariSeq TB is a purpose-built bioinformatics pipeline developed by ClariSeq Analytics. It allows clinicians, researchers and other users to identify the Mycobacterium tuberculosis complex with resolution of 8 MTBC candidate species, with lineage and spoligotypes. It also allows detection of non-tuberculous mycobacteria (NTM) with species-level identification of 116 NTM species.

The platform takes simple input of raw FASTQ files and provides quick analysis to perform species ID and MTB drug-resistance identification across 20 drugs. Furthermore, ClariSeq TB generates CG view maps, allowing researchers to publish high-quality research. An innovative statistical dashboard lets you analyze your sample cohorts and perform real-time interpretation of trends.

Features

From WGS data to actionable insights

Explore the core capabilities built into ClariSeq TB.

01

Species ID and Lineage
with Spoligotypes

Accurate identification of MTB, NTM and lineage calling from WGS data.

MTB · NTM · Lineage · Spoligotype
02

Drug Resistance

Comprehensive resistance profiling based on WHO, CRyPTIC and published literature.

20 Drugs · 55 Genes
03

CG View

Interactive circular genome map with coverage and gene rings.

Genome · Coverage · Gene Rings
04

Insights

Clear visualizations and statistical insights to monitor and understand your results.

Samples · Resistance · Trends

Start Virtual Tour

A guided virtual tour of ClariSeq TB, from a finished run to the drug-resistance report and cohort insights.

Demo workspace · illustrative data

See ClariSeq TB in action

The Clinical Burden of MTB

Key facts from the WHO and India’s Ministry of Health, and why whole-genome sequencing matters.

Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis (MTB). According to the WHO, it is the world’s leading cause of death from a single infectious agent.

Worldwide, 2024

10.7 million

people fell ill with TB

1.23 million

people died from TB

390,000

people developed drug-resistant TB (MDR/RR-TB)

2 in 5

people with drug-resistant TB accessed treatment

Drug resistance makes TB harder to treat. The drugs must match the bacteria, and resistant TB needs longer and more complex treatment. In 2024, 3.2% of new TB cases and 16% of previously treated cases had rifampicin-resistant or multidrug-resistant TB (MDR/RR-TB).

India, 2024

2.7 million

estimated new TB cases, about 1 in 4 of the world's cases (25%)

187 per lakh

people fell ill, down 21% from 237 per lakh in 2015

32%

of the world's drug-resistant TB (MDR/RR-TB) is in India

26.18 lakh

people diagnosed in 2024, with over 92% treatment coverage

India has made real progress: TB incidence has fallen 21% since 2015, almost double the global fall of 12%. But India still has the largest number of TB cases and of drug-resistant TB in the world.

Why whole-genome sequencing helps monitor TB

Rapid molecular tests check only a few drugs, and culture-based drug testing can take weeks because MTB grows slowly. Whole-genome sequencing (WGS) reads the full genome of the bacteria from a single sample. From that one data set, a lab can report:

  • The species. It confirms whether the bacteria are in the MTB complex or are non-tuberculous mycobacteria (NTM), which need different treatment.
  • Resistance across many drugs. It finds mutations linked to resistance to first-line and second-line drugs together, read against the WHO catalogue of mutations.
  • Resistance that is just starting. When sequencing depth is high enough, small groups of resistant bacteria can be seen, so a treatment plan can be reviewed early.
  • Lineage and spoligotype. These show which type of MTB a patient has and let labs compare strains.
  • Relapse or new infection. Comparing genomes from repeat samples helps show whether the same strain came back or a different one infected the patient.
  • Spread in the community. Very similar genomes point to recent transmission, which helps public health teams find and stop clusters.

The WHO now recommends sequencing-based tests for drug-resistant TB (targeted next-generation sequencing, 2024 guidance) and keeps a catalogue of resistance mutations (2023 edition) so results can be read the same way everywhere.

ClariSeq TB analyses WGS data against that catalogue, the CRyPTIC compendium and curated literature. Sequencing results support clinical judgement and do not replace confirmatory testing.

Sources: WHO tuberculosis fact sheet; WHO Global Tuberculosis Report 2025, drug-resistant TB (data for 2024); Ministry of Health and Family Welfare, India, on the WHO report (November 2025); WHO on targeted next-generation sequencing (March 2024).

Get Started

From raw FASTQ to a
drug-resistance report, start today.

Create an account, upload your sequencing files, and get species ID,
lineage and drug-resistance results in one dashboard.

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Frequently asked questions

What is ClariSeq TB?

ClariSeq TB is a purpose-built bioinformatics pipeline by ClariSeq Analytics that identifies Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) species and reports drug resistance from raw whole-genome sequencing data.

What input does ClariSeq TB need?

Raw FASTQ files from whole-genome sequencing (WGS), including shotgun WGS. ClariSeq TB currently supports short-read data from Illumina, BGI and MGI platforms, as paired-end or single-end reads. Long-read data, such as Oxford Nanopore, is not currently supported. Upload your files and ClariSeq TB runs species identification and drug-resistance analysis, returning the results in a single dashboard.

Which mycobacterial species can ClariSeq TB identify?

It resolves 8 MTBC candidate species, with lineage and spoligotypes, and identifies 116 non-tuberculous mycobacteria (NTM) species at species level.

How many drugs does the MTB drug-resistance analysis cover?

20 drugs. Each mutation is checked against the WHO 2023 catalogue, the CRyPTIC compendium and a curated literature database, and each source keeps its own independent call.

What are CG view maps?

CG view maps are circular genome maps generated by ClariSeq TB, showing coverage and genes, so researchers can produce figures for publication.