Enterprise-Grade NGS BioIT with Speed, Scalability, and Reliability



Accelerate your existing pipelines from FASTQ, BAM, to VCF

4 Hours

BWA/GATK4 industry best practice WGS turnaround with no downsampling


Computing and management cost savings in the cloud

How It Works


Workload Parallelization

  • Orchestrate a complex string of analysis tools and heterogeneous big data flow to a fast, reliable production workflow based on GATK4 Best Practices.

  • Design your own pipelines for optimal performance and results by chromosomes, contiguous unambiguous regions, discordant, soft-clipped reads, or coding regions with predictable turnaround.

One-Click Job Submission

  • Manage and run your jobs from a streamlined and informative web-based user interface with automatic resource scheduling to maximize workflow performance under the hood.

  • Analyze multiple samples at once to ensure run-to-run configuration consistency with no big data hassle.

Data Cloud

Self-Service, On-demand Computing

  • Containerize your sequencing analysis tools on Docker and quickly run them on the Atgenomix cloud HPC environment.

  • A simple, yet powerful BioIT automation that takes the complexity out of IT environments and accelerates genomics initiatives.


Featured Pipelines

Read Mapping

Germline Analysis

  • DeepVariant germline SNPs and indels variant calling by deep neural network

  • GATK4 HaplotypeCaller germline SNPs and indels calling via local re-assembly of haplotypes

  • DELLY2 structural variant discovery by integrated paired-end and split-read analysis

Tumor-Normal Somatic Analysis

  • Mutect2 somatic SNVs and indels calling via local assembly of haplotypes

  • Varscan2 somatic mutation calling for targeted, exome, and whole-genome resequencing data

  • DELLY2 somatic structural variant discovery by integrated paired-end and split-read analysis

RNA-Seq Analysis

  • Star 2-pass spliced transcript alignment

  • Cufflinks transcriptome assembly and differential expression analysis

Other Analysis


Integrated Storages


Hadoop DFS

Primary distributed file system using commodity hardware


Intel Lustre

Parallel file system that supports specialized requirements of HPC simulation environments

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Azure Data Lake Storage

Online file storage web service for storing and accessing data on Microsoft Azure Data Lake Storage Gen2

Man Hands On Keyboard

Simple, agentless Bio-IT automation with Docker. Your secure and enterprise private cloud on Microsoft Azure.