atgenomix

deepvariant-on-spark

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

graphseq

String Graph Construction on Spark

connectedreads

a machine-learning optimized long-range genome analysis workflow for next-generation sequencing

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

hail

Scalable genomic data analysis.

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

JSON-schemas

JSON schemas for genomics and health data exchange and forms

seqslab-api-reference

SeqsLab REST API YAML files for docs.atgenomix.com

seqslab-connector

SeqsLab cluster and data lakehouse connector for Python

seqslab-docs-operator-pipeline-api

API docs for SeqsLab operator pipeline in distributed workflow execution

seqslab-operators

Atgenomix Operators are SeqsLab platform plugins and open-source Cromwell extensions that streamline heterogeneous data integration and transformation, and scale complex workflow tasks, using distributed computing clusters and GPU accelerators.

spark-operator

Kubernetes operator for managing the lifecycle of Apache Spark applications on Kubernetes.

superset

Apache Superset is a Data Visualization and Data Exploration Platform

support

workflow-execution-service-schemas

The WES API is a standard way to run and manage portable workflows.

assets

sample-sheet

Parse Illumina sample sheets with Python