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[ADAM-1832] Use awesome list style and link to bigdatagenomics/awesome-adam. #1879

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[ADAM-1832] Use awesome list style and link to bigdatagenomics/awesome-adam. #1879

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30 changes: 16 additions & 14 deletions README.md
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Expand Up @@ -96,23 +96,25 @@ platforms.

There are a number of tools built using ADAM's core APIs:

- [Avocado](https://github.com/bigdatagenomics/avocado) is a variant caller built
on top of ADAM for germline and somatic calling
- [Cannoli](https://github.com/bigdatagenomics/cannoli) uses ADAM's [pipe](#pipes)
API to parallelize common single-node genomics tools (e.g.,
* [Avocado](https://github.com/bigdatagenomics/avocado) - Avocado is a distributed
variant caller built on top of ADAM for germline and somatic calling.
* [Cannoli](https://github.com/bigdatagenomics/cannoli) - ADAM
[Pipe](http://adam.readthedocs.io/en/latest/api/pipes/) API wrappers for bioinformatics
tools, (e.g.,
[BWA](https://github.com/lh3/bwa),
[bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml),
[FreeBayes](https://github.com/ekg/freebayes))
- [DECA](https://github.com/bigdatagenomics/deca) is a reimplementation of the
XHMM copy number variant caller on top of ADAM/Apache Spark
- [Gnocchi](https://github.com/bigdatagenomics/gnocchi) provides primitives for
running GWAS/eQTL tests on large genotype/phenotype datasets using ADAM
- [Lime](https://github.com/bigdatagenomics/lime) provides a parallel
implementation of genomic set theoretic primitives using the [region join
API](#join)
- [Mango](https://github.com/bigdatagenomics/mango) is a library for visualizing
large scale genomics data with interactive latencies and serving data using the
[GA4GH schemas](https://github.com/ga4gh/schemas)
* [DECA](https://github.com/bigdatagenomics/deca) - DECA is a reimplementation of the
XHMM copy number variant caller on top of ADAM.
* [Gnocchi](https://github.com/bigdatagenomics/gnocchi) - Gnocchi provides primitives
for running GWAS/eQTL tests on large genotype/phenotype datasets using ADAM.
* [Lime](https://github.com/bigdatagenomics/lime) - Lime provides a
parallel implementation of genomic set theoretic primitives using the ADAM
[region join](http://adam.readthedocs.io/en/latest/api/joins/) API.
* [Mango](https://github.com/bigdatagenomics/mango) - Mango is a library for
visualizing large scale genomics data with interactive latencies.
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Maybe we could add some of your adam examples and some of @antonkulaga's codes? Also @ryan-williams?

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The idea is that it is easier to pull request against the separate awesome-adam repo than pull request here.

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Oh, sorry about that, I totally missed that. Yes, you are correct!


For more, please see our [awesome list of applications](https://github.com/bigdatagenomics/awesome-adam) that extend ADAM.


# Connecting with the ADAM team
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35 changes: 17 additions & 18 deletions docs/index.rst
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As the diagram shows, beyond the `ADAM CLI <#cli>`__, there are a number
of tools built using ADAM's core APIs:

- `Avocado <https://github.com/bigdatagenomics/avocado>`__ is a variant
caller built on top of ADAM for germline and somatic calling
- `Cannoli <https://github.com/bigdatagenomics/cannoli>`__ uses ADAM's
`pipe <#pipes>`__ API to parallelize common single-node genomics
tools (e.g., `BWA <https://github.com/lh3/bwa>`__,
- `Avocado <https://github.com/bigdatagenomics/avocado>`__ - Avocado is a distributed
variant caller built on top of ADAM for germline and somatic calling.
- `Cannoli <https://github.com/bigdatagenomics/cannoli>`__ - ADAM
`Pipe <#pipes>`__ API wrappers for bioinformatics tools, (e.g.,
`BWA <https://github.com/lh3/bwa>`__,
`bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`__,
`FreeBayes <https://github.com/ekg/freebayes>`__)
- `DECA <https://github.com/bigdatagenomics/deca>`__ is a
reimplementation of the XHMM copy number variant caller on top of
ADAM/Apache Spark
- `Gnocchi <https://github.com/bigdatagenomics/gnocchi>`__ provides
primitives for running GWAS/eQTL tests on large genotype/phenotype
datasets using ADAM
- `Lime <https://github.com/bigdatagenomics/lime>`__ provides a
parallel implementation of genomic set theoretic primitives using the
`region join API <#join>`__
- `Mango <https://github.com/bigdatagenomics/mango>`__ is a library for
visualizing large scale genomics data with interactive latencies and
serving data using the `GA4GH
schemas <https://github.com/ga4gh/schemas>`__
- `DECA <https://github.com/bigdatagenomics/deca>`__ - DECA is a reimplementation of the
XHMM copy number variant caller on top of ADAM.
- `Gnocchi <https://github.com/bigdatagenomics/gnocchi>`__ - Gnocchi provides primitives
for running GWAS/eQTL tests on large genotype/phenotype datasets using ADAM.
- `Lime <https://github.com/bigdatagenomics/lime>`__ - Lime provides a
parallel implementation of genomic set theoretic primitives using the ADAM
`region join <#join>`__ API.
- `Mango <https://github.com/bigdatagenomics/mango>`__ - Mango is a library for
visualizing large scale genomics data with interactive latencies.

For more, please see our `awesome list of applications <https://github.com/bigdatagenomics/awesome-adam>`__ that extend ADAM.


.. toctree::
:caption: Architecture
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