ATGENOMIX SEQSLAB

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

10X

Accelerate your existing pipelines from FASTQ, BAM, to VCF

4 Hours

BWA/GATK4 industry best practice WGS turnaround with no downsampling

50%

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.

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

BWA MEM alt-aware alignment
Complete GRCh38 reference including alternative sequences, plus decoys and HLA
GRCh37 (hg19) reference

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

GATK4 GenotypeGVCFs joint genotyping on gVCF files produced by HaplotypeCaller
WhatsHap haplotype assembly

Integrated Storages

Hadoop DFS

Primary distributed file system using commodity hardware

Intel Lustre

Parallel file system that supports specialized requirements of HPC simulation environments

Azure Data Lake Storage

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

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

Test Drive