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42 changes: 20 additions & 22 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/[email protected]" alt="TileDB logo" width="400"></a>
<a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/main/doc/source/_static/[email protected]" alt="TileDB logo" width="400"></a>

[![Build Status](https://img.shields.io/azure-devops/build/tiledb-inc/836549eb-f74a-4986-a18f-7fbba6bbb5f0/8/main?label=Azure%20Pipelines&logo=azure-pipelines&style=flat-square)](https://dev.azure.com/TileDB-Inc/CI/_build/latest?definitionId=8&branchName=main)
[![Docker-CLI](https://img.shields.io/static/v1?label=Docker&message=tiledbvcf-cli&color=099cec&logo=docker&style=flat-square)](https://hub.docker.com/repository/docker/tiledb/tiledbvcf-cli)
Expand All @@ -12,7 +12,7 @@ A C++ library for efficient storage and retrieval of genomic variant-call data u

- Easily ingest large amounts of variant-call data at scale
- Supports ingesting single sample VCF and BCF files
- New samples are added *incrementally*, avoiding computationally expensive merging operations
- New samples are added _incrementally_, avoiding computationally expensive merging operations
- Allows for highly compressed storage using TileDB sparse arrays
- Efficient, parallelized queries of variant data stored locally or remotely on S3
- Export lossless VCF/BCF files or extract specific slices of a dataset
Expand All @@ -24,9 +24,9 @@ A C++ library for efficient storage and retrieval of genomic variant-call data u

## Quick Start

The [documentation website][vcf] provides comprehensive usage examples but here are a few quick exercises to get you started.
The [TileDB Academy][vcf] provides comprehensive usage examples but here are a few quick exercises to get you started.

We'll use a dataset that includes 20 synthetic samples, each one containing over 20 million variants. We host a publicly accessible version of this dataset on S3, so if you have TileDB-VCF installed and you'd like to follow along just swap out the `uri`'s below for `s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20`. And if you *don't* have TileDB-VCF installed yet, you can use our [Docker images](docker/README.md) to test things out.
We'll use a dataset that includes 20 synthetic samples, each one containing over 20 million variants. We host a publicly accessible version of this dataset on S3, so if you have TileDB-VCF installed and you'd like to follow along just swap out the `uri`'s below for `s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20`. And if you _don't_ have TileDB-VCF installed yet, you can use our [Docker images](docker/README.md) to test things out.

### CLI

Expand Down Expand Up @@ -84,30 +84,28 @@ returns results as a pandas `DataFrame`

## Want to Learn More?


* [Blog "Population Genomics is a Data Management Problem"][blog]
* [Check out the full documentation][vcf]
* [Why use TileDB-VCF?][docswhytile]
* [Data Model][docsdatamodel]
* [Installation][docsinstallation]
* [How To][docshowto]
* [Reference][docsreference]

- [Blog "Population Genomics is a Data Management Problem"][blogdatamgmt]
- [Blog "TileDB 101: Population Genomics"][blogpopgen101]
- [Check out the TileDB Academy][vcf]
- [Data Model][docsdatamodel]
- [Installation][docsinstallation]
- [Tutorials][docstutorials]
- [API Reference][docsreference]

# Code of Conduct

All participants in TileDB spaces are expected to adhere to high standards of
professionalism in all interactions. This repository is governed by the
specific standards and reporting procedures detailed in depth in the
[TileDB core repository Code Of Conduct](
https://github.com/TileDB-Inc/TileDB/blob/dev/CODE_OF_CONDUCT.md).
[TileDB core repository Code Of Conduct](https://github.com/TileDB-Inc/TileDB/blob/dev/CODE_OF_CONDUCT.md).

<!-- links -->

[tiledb]: https://github.com/TileDB-Inc/TileDB
[vcf]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics
[docswhytile]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics#why-use-tiledb-vcf
[docsdatamodel]: https://docs.tiledb.com/main/integrations-and-extensions/population-genomics/data-model
[docsinstallation]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/installation
[docshowto]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/how-to
[docsreference]: https://docs.tiledb.com/main/integrations-and-extensions/genomics/population-genomics/api-reference
[blog]: https://tiledb.com/blog/population-genomics-is-a-data-management-problem
[vcf]: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/
[docsdatamodel]: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/foundation/data-model/
[docsinstallation]: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/quickstart/#installation
[docstutorials]: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/tutorials/
[docsreference]: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/api-reference/
[blogdatamgmt]: https://tiledb.com/blog/population-genomics-is-a-data-management-problem
[blogpopgen101]: https://tiledb.com/blog/tiledb-101-population-genomics