https://github.com/bigdatagenomics/avocado

A Variant Caller, Distributed. Apache 2 licensed.
https://github.com/bigdatagenomics/avocado

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A Variant Caller, Distributed. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/bigdatagenomics/avocado
• Owner: bigdatagenomics
• License: apache-2.0
• Created: 2013-09-10T21:44:45.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2019-03-11T21:33:58.000Z (over 5 years ago)
• Last Synced: 2024-06-30T20:37:45.731Z (3 months ago)
• Language: Scala
• Homepage: http://bdgenomics.org/projects/avocado/
• Size: 2.24 MB
• Stars: 71
• Watchers: 22
• Forks: 42
• Open Issues: 25
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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# A Variant Caller, Distributed

This README represents the TL;DR docs for avocado. More detailed documentation

is hosted at [Read the Docs](http://bdg-avocado.readthedocs.io/).

# Who/What/When/Where/Why avocado?

Avocado is a distributed variant caller built on top of the [ADAM format and

APIs](http://www.github.com/bigdatagenomics/adam) and [Apache

Spark](http://spark.apache.org/). Avocado is an open source project and is

released under the [Apache 2.0 license](https://github.com/bigdatagenomics/avocado/blob/master/LICENSE).

Avocado can be used for single sample germline variant calling, trio calling,

and joint variant calling. Avocado has >99% SNP calling accuracy, and >96%

INDEL calling accuracy when paired with ADAM's INDEL realignment pipeline.

When run on a single 32 core machine, Avocado can call variants on a 60x

coverage whole genome sequencing (WGS) dataset in approximately 7 hours. By

using Apache Spark to scale across multiple machines, Avocado can process the

same WGS dataset in approximately 15 minutes when using 1,024 cores.

# How avocado?

## Building Avocado

Avocado uses [Maven](http://maven.apache.org/) to build. To build avocado, cd

into the repository and run "mvn package".

## Avocado binaries

Nightly builds of Avocado are available from the [OSS Sonatype

repository](https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/avocado/).

Additionally, we make a Docker image available from [Quay](https://quay.io/repository/ucsc_cgl/avocado?tag=latest&tab=tags).

# License

ADAM is released under the [Apache License, Version 2.0](LICENSE.txt).

# Citing Avocado

Avocado has been described in a PhD thesis. To cite this thesis, please cite:

```

@article{nothaft17,

  title={Scalable Systems and Algorithms for Genomic Variant Analysis},

  author={Nothaft, Frank Austin},

  school = {EECS Department, University of California, Berkeley},

  uear = {2017},

  month = {Dec},

  URL = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-204.html},

  number = {UCB/EECS-2017-204}

}

```

A preprint describing Avocado should be released by the end of January 2018.