From d20a9eed89b15100b3e2efdfb48efca7131f5e1d Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 19 Jan 2018 17:28:56 -0500 Subject: [PATCH] Use awesome list style and link to bigdatagenomics/awesome-adam. --- README.md | 30 ++++++++++++++++-------------- docs/index.rst | 35 +++++++++++++++++------------------ 2 files changed, 33 insertions(+), 32 deletions(-) diff --git a/README.md b/README.md index 3c28ce34da..154290dd31 100644 --- a/README.md +++ b/README.md @@ -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. + +For more, please see our [awesome list of applications](https://github.com/bigdatagenomics/awesome-adam) that extend ADAM. # Connecting with the ADAM team diff --git a/docs/index.rst b/docs/index.rst index 3f5dc6a5c1..ea7801ba45 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -36,26 +36,25 @@ found below. As the diagram shows, beyond the `ADAM CLI <#cli>`__, there are a number of tools built using ADAM's core APIs: -- `Avocado `__ is a variant - caller built on top of ADAM for germline and somatic calling -- `Cannoli `__ uses ADAM's - `pipe <#pipes>`__ API to parallelize common single-node genomics - tools (e.g., `BWA `__, +- `Avocado `__ - Avocado is a distributed + variant caller built on top of ADAM for germline and somatic calling. +- `Cannoli `__ - ADAM + `Pipe <#pipes>`__ API wrappers for bioinformatics tools, (e.g., + `BWA `__, `bowtie2 `__, `FreeBayes `__) -- `DECA `__ is a - reimplementation of the XHMM copy number variant caller on top of - ADAM/Apache Spark -- `Gnocchi `__ provides - primitives for running GWAS/eQTL tests on large genotype/phenotype - datasets using ADAM -- `Lime `__ provides a - parallel implementation of genomic set theoretic primitives using the - `region join API <#join>`__ -- `Mango `__ is a library for - visualizing large scale genomics data with interactive latencies and - serving data using the `GA4GH - schemas `__ +- `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 <#join>`__ API. +- `Mango `__ - Mango is a library for + visualizing large scale genomics data with interactive latencies. + +For more, please see our `awesome list of applications `__ that extend ADAM. + .. toctree:: :caption: Architecture