DEEPCHEK® SOFTWARE

Downstream Sequencing Data Analysis and Interpretation Software

Description

DeepChek® is a downstream analysis software developed by ABL, able to handle sequencing data and intended to be used for performing genomic data analyses (genotyping, subtyping, amino-acid mutations detection, nucleotide changes characterization…) and clinical interpretations (drug resistance, vaccine escape, disease prognosis…).

Compatible with Electrophoresis Capillary and Next Generation Sequencing (NGS) platforms (like MiSeq, MiniSeq, Ion Torrent, PGM, S5, 454-Junior, 454-FLX…), DeepChek® is available for different applications (HIV, HBV, HCV, CMV, HPV…), stores, organizes sequencing data in a dedicated database format. Depending on the application, on the type of sequencing platform and based on the requirements from end users, it performs several types of analyses, interpretations and is able to generate reports to be used either for research or for routine use.

  • Supported formats: AB1, FASTA and PLAIN-TEXT for Sanger, FASTA/FASTQ (including paired sequencing), BAM/SAM for NGS covering Targeted Genes or also compatible with Whole Genome data.
  • Examples of analyses: genotyping, high-resolution subtyping, variants calling…
  • Examples of interpretations: drug resistance, disease prognosis, …
  • Included services: updates/upgrades (quarterly releases), support, web-training, historical sequencing data import
  • On-demand services: local training, integration with third-party instruments or systems, customization…

The DeepChek® software system is a secured web application which can be used through a Cloud access or locally, through pre-configured servers. It is made available with regular updates (new clinical databases, guidelines…) and quarterly upgrades (new features, modules, applications…) and can be fully integrated within the IT network of each laboratory (integration with the sequencing platform, with the Laboratory Information System – LIS, with the Hospital Information System – HIS…).

The DeepChek®-HIV and DeepChek®-HBV/HCV applications are CE-IVD (LU/CA01/IVD/69).

Overview of the pipeline

Examples of reports

Downloads

General documentation

  • Quick start guide

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  • Implementation options

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Posters

  • Implementation of Next-Generation Sequencing for Hepatitis B Resistance and Genotyping in a Clinical Laboratory

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  • Use of Next-Generation Sequencing Technologies in the Clinical HIV Laboratory

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  • Next Generation Sequencing for HIV virus genotyping and detection of antiviral resistance

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  • Clinical impact of Ultra-Deep Versus Sanger Sequencing detection of minority mutations on the HIV-1 [...]

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  • An End-To-End Solution in Deep Sequencing of HIV: Sensitive Detection of HIV-1 Genomic Variations Combined with [...]

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  • Hepatitis C Virus High Resolution Subtyping Using Next Generation Sequencing (NGS) Data

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  • A Novel Software and Database Solution Tool for Analysis of Sanger and Next Generation Sequencing (NGS)

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  • Advanced Medical Devices for HCV High Resolution Subtyping, Genotyping and Drug Resistance Testing [...]

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  • Use of Illumina MiSeq Technology to Detect Drug Resistance Mutations in Human Cytomegalovirus

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  • Use of DeepChek® v1.1 and VisibleChek® for the analysis and integration of 454 GS Junior data from the RT and Protease of HIV-1

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  • Advanced Medical Devices for HBV Genotyping, Drug Resistance Testing and Detection of Surface Antigen Mutants Using [...]

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  • Next-Generation Sequencing Technology in the Clinical HIV Laboratory: A More Sensitive Alternative to Sanger Sequencing

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  • DeepChek® HIV v1.0., a reliable tool for the bioinformatics analysis and resistance interpretation of Massive Ultra Deep [...]

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  • Detection of Minority HIV-1 Drug-Resistant Variants Moderately Improves the Prediction of Salvage Antiretroviral [...]

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  • Added value of Ultra Deep Sequencing in patients with HIV-1 Transmitted Drug Resistance mutations [...]

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  • A Fully Integrated and Simplified HIV Clinical Genotyping Solution Using 454 Ultra-Deep-Sequencing and [...]

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Papers

  • Minority resistant HIV-1 variants and the response to first-line NNRTI therapy

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  • High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

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  • Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance [...]

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  • COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification

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  • Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene [...]

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