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adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

airiot

Distributed commonsense AI reasoning framework for IoT applications

amiss

deepvariant

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

dhpgindex

This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

gatk

Official code repository for GATK versions 4 and up

hadoop-bam

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

histoprep

Preprocessing module for large histological images

oncodash

Clinical oncology tumor board decision support system made by the Decider project.

pangenspark

Scalable reference genome assembly from compressed pan-genome index with Spark

schema

SCHeMa (Scheduler for scientific Containers on clusters of Heterogeneous Machines) an open source platform to facilitate the execution and reproducibility of computational experiments on heterogeneous clusters.

seqpig

SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data.

sparkbeagle

SparkBeagle: scalable distributed genotype imputation in the cloud

tns-windmeter

TNS windmeter project

virapipe

ViraPipe is a Apache Spark based scalable pipeline for metagenome analysis from NGS read data