Skip to content

Commit

Permalink
Arriba 1.0.0
Browse files Browse the repository at this point in the history
  • Loading branch information
suhrig committed Oct 14, 2018
1 parent 141b57d commit d4bec52
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 4 deletions.
6 changes: 3 additions & 3 deletions documentation/quickstart.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@ Arriba has only a single prerequisite: [STAR](https://github.com/alexdobin/STAR)
Compile the latest stable version of Arriba or use the precompiled binaries in the download file. **Note: You should not use `git clone` to download Arriba, because the git repository does not include the blacklist! Instead, download the latest tarball from the [releases page](https://github.com/suhrig/arriba/releases/) as shown here:**

```bash
wget https://github.com/suhrig/arriba/releases/download/v0.12.0/arriba_v0.12.0.tar.gz
tar -xzf arriba_v0.12.0.tar.gz
cd arriba_v0.12.0 && make # or use precompiled binaries
wget https://github.com/suhrig/arriba/releases/download/v1.0.0/arriba_v1.0.0.tar.gz
tar -xzf arriba_v1.0.0.tar.gz
cd arriba_v1.0.0 && make # or use precompiled binaries
```

Arriba requires an assembly in FastA format, gene annotation in GTF format, and a STAR index built from the two. You can use your preferred assembly and annotation, as long as their coordinates are compatible with hg19/hs37d5/GRCh37 or hg38/GRCh38. Support for mm10 is in development. If you use another assembly, then the coordinates in the blacklist will not match and the predictions will contain many false positives. GENCODE annotation is recommended over RefSeq due to more comprehensive annotation of splice-sites, which improves sensitivity. If you do not already have the files and a STAR index, you can use the script `download_references.sh`. It downloads the files to the current working directory and builds a STAR index. Run the script without arguments to see a list of available files. Note that this step requires ~30 GB of RAM and 8 cores (or whatever number of cores you pass as the second argument).
Expand Down
2 changes: 1 addition & 1 deletion source/options.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
using namespace std;

const string HELP_CONTACT = "https://github.com/suhrig/arriba/";
const string ARRIBA_VERSION = "0.12.0";
const string ARRIBA_VERSION = "1.0.0";

string wrap_help(const string& option, const string& text, const unsigned short int max_line_width = 80);

Expand Down

0 comments on commit d4bec52

Please sign in to comment.