Refgenie and bioconductor | Databio Slides

# Refgenie and bioconductor

Nathan Sheffield

<span style="font-size:0.6em"><a href="http://www.databio.org/slides">www.databio.org/slides</a></span>

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# Refgenie and bioconductor

## The problem

Many tools require genome-related assets (like indexes).

How should we organize these on disk?

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## A standard organization simplifies tool interface

```
pipeline.py --genome hg38
```

```
pipeline.py --bowtie2-index path/to/hg38/bowtie2-index \
  --tss_annotation path/to/hg38/tss_annotation.bed \
  --ensembl_anno path/to/hg38/ensembl_v86.gtf
```

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## Illumina's iGenomes is one answer

iGenomes is *a collection of reference sequences and annotation files for commonly analyzed organisms*.

You download a tarball of a standard structure for your genome of interest, then write tools off that.

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## The 'central repository' approach is limited

- *Not scripted.* No iGenomes for an arbitrary genome/asset.
- *Not modular*. No access to individual assets.
- *Not programmatic*. Can't access data/metadata via API.

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## Refgenie solves these limitations

- *Two ways to retrieve an asset.*
  - `build` any asset from a recipe.
  - `pull` any individual asset from a server
- *Better discoverability*.
  - `list/listr` shows assets
  - `refgenieserver` is a browseable web interface and API
- *Managed locations*.
  - `seek` returns the local path to assets
  - `add/remove` to manage your own assets

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## Refgenie CLI example

```
refgenie pull hg38/fasta
refgenie build hg38/bowtie2_index
refgenie seek hg38/bowtie2_index
```

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## Using Refgenie from R

```
mod = reticulate::import("refgenconf", convert=FALSE)
rgc = mod$RefGenConf(Sys.getenv("REFGENIE"))
rgc$pull("hg38", "bowtie2_index", "default")
rgc$seek("hg38", "bowtie2_index"))
```

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## Resources

- These slides: [databio.org/slides](https://databio.org/slides)
- Refgenie documentation: [refgenie.databio.org](https://refgenie.databio.org)
- Refgenieserver instance: [refgenomes.databio.org](https://refgenomes.databio.org)
- GitHub: [github.com/databio/refgenie](https://github.com/databio/refgenie/)

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# Thank You

<span class="small bullet"><img src="/images/external/github_bug_black.svg" height="20" class="bullet"><a href="http://github.com/nsheff">nsheff</a></span> &middot;
<span class="small bullet"><img src="/images/icons/web.svg" height="25" class="bullet"><a href="http://databio.org">databio.org</a></span> &middot;
<span class="small bullet"><img src="/images/icons/letter.svg" height="25" class="bullet"><a href="mailto:nsheffield@virginia.edu">nsheffield@virginia.edu</a></span>

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