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Architecture

  • Architecture Overview
  • The ADAM Stack Model
  • The bdg-formats schemas
  • Interacting with data through ADAM’s evidence access layer

Installation

  • Building ADAM from Source
  • Installing ADAM using Pip
  • Running an example command

Benchmarking

  • Benchmarks
  • Storage Size

Deploying ADAM

  • Deploying ADAM on AWS
  • Running ADAM on CDH 5, HDP, and other YARN based Distros
  • Running ADAM on Toil
  • Running ADAM on Slurm

The ADAM CLI

  • Running ADAM’s command line tools
  • Action tools
  • Conversion tools
  • Printing tools

ADAM's APIs

  • API Overview
  • Loading data with the ADAMContext
  • Working with genomic data using GenomicDatasets
  • Using ADAM’s RegionJoin API
  • Using ADAM’s Pipe API
  • ADAM Python Documentation

Building Downstream Applications

  • Building Downstream Applications
  • Extend the ADAM CLI by adding new commands
  • Extend the ADAM CLI by adding new commands in an external repository
  • Use ADAM as a library in new applications

Algorithms in ADAM

  • Core Algorithms
  • BQSR Implementation
  • Indel Realignment Implementation
  • Duplicate Marking Implementation
  • ShuffleRegionJoin Load Balancing

References

  • Citing ADAM
  • References
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