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lcoombe authored Jun 29, 2021
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Expand Up @@ -16,13 +16,27 @@ Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL and Birol I. LongStitch: Hig


### Dependencies
* GNU Make
* [Tigmint](https://github.com/bcgsc/tigmint) v1.2.4+
* [ntLink](https://github.com/bcgsc/ntLink) v1.0.0+
* [ARCS/ARKS](https://github.com/bcgsc/arcs) v1.2.2+
* [ABySS](https://github.com/bcgsc/abyss) v2.3.0+
* [LINKS](https://github.com/bcgsc/links) v1.8.5+
* [samtools](http://www.htslib.org/)

All dependencies for LongStitch are available in conda and homebrew.

_Installing dependencies with conda:_
```
conda install -c bioconda tigmint ntlink arcs samtools
```

_Installing dependencies with homebrew:_
```
brew tap brewsci/bio
brew install tigmint ntlink arcs
```

### Example command
For example, to run the default pipeline on a draft assembly `draft-assembly.fa` with the reads `reads.fa.gz` and a genome size of `gsize`:
```
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