Awesome ADAM

Awesome list of applications that extend the Big Data Genomics ADAM genomics analysis platform.

Table of Contents

• Extending ADAM
  • Applications
  • Examples
  • Libraries

Extending ADAM

Applications

• Avocado - Avocado is a distributed variant caller built on top of ADAM for germline and somatic calling.
• Cannoli - ADAM Pipe API wrappers for bioinformatics tools, (e.g., BWA, bowtie2, FreeBayes)
• DECA - DECA is a reimplementation of the XHMM copy number variant caller on top of ADAM.
• Gnocchi - Gnocchi provides primitives for running GWAS/eQTL tests on large genotype/phenotype datasets using ADAM.
• Lime - Lime provides a parallel implementation of genomic set theoretic primitives using the ADAM region join API.
• Mango - Mango is a library for visualizing large scale genomics data with interactive latencies.

Examples

• adam-commands - External commands in Java and Scala for ADAM.
• adam-examples - Examples in Java and Scala for ADAM.

Libraries

• adam-explorer - Interactive explorer for ADAM genomics data models.
• biojava-adam - Biojava and ADAM integration, including support for reading Genbank DNA and Protein sequences.
• gfa-adam - Graphical Fragment Assembly (GFA) support for ADAM.

License