https://github.com/illumina/slimcache
Nirvana tool that creates RefSeq- or Ensembl-specific cache files
https://github.com/illumina/slimcache
Last synced: 3 months ago
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Nirvana tool that creates RefSeq- or Ensembl-specific cache files
- Host: GitHub
- URL: https://github.com/illumina/slimcache
- Owner: Illumina
- License: gpl-3.0
- Created: 2021-01-27T17:43:03.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-04-23T17:21:22.000Z (about 4 years ago)
- Last Synced: 2025-01-24T09:27:39.886Z (5 months ago)
- Language: C#
- Size: 62.5 KB
- Stars: 0
- Watchers: 9
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# SlimCache
SlimCache is standalone tool that creates a new set of Nirvana cache files containing only transcripts from the desired transcript source.
## Building
Remember to clone the git repo using the recursive option - this will automatically handle the Nirvana submodule:
```
git clone --recursive https://github.com/Illumina/SlimCache.git
```
After that, build the solution using the [.NET 5.0 SDK](https://dotnet.microsoft.com/download/dotnet/5.0):
```
cd SlimCache
dotnet build -c Release
```
## Prerequisites
Using the paths to your Nirvana 3.9 or later cache and reference files, use the following command to create a new set of cache files:
## Creating RefSeq-Only Cache Files
```
USAGE: SlimCache.dll
```
```bash
dotnet SlimCache.dll \
Cache/GRCh37/Both \
References/Homo_sapiens.GRCh37.Nirvana.dat \
Cache/GRCh37/RefSeq \
RefSeq
```
When this command is run, the following output is displayed:
```bash
- loading reference sequence... finished.
- loading cache... finished.
- filtering transcripts... 196,520 transcripts removed.
- removing duplicate predictions... 101,180 predictions removed.
- writing SIFT prediction cache... finished.
- writing PolyPhen prediction cache... finished.
- writing transcript cache... finished.
Peak memory usage: 1.407 GB
```
## Creating Ensembl-Only Cache Files
```bash
dotnet SlimCache.dll \
Cache/GRCh37/Both \
References/Homo_sapiens.GRCh37.Nirvana.dat \
Cache/GRCh37/Ensembl \
Ensembl
```
When this command is run, the following output is displayed:
```bash
- loading reference sequence... finished.
- loading cache... finished.
- filtering transcripts... 64,624 transcripts removed.
- removing duplicate predictions... 3,438 predictions removed.
- writing SIFT prediction cache... finished.
- writing PolyPhen prediction cache... finished.
- writing transcript cache... finished.
Peak memory usage: 1.927 GB
```