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Test README fixes
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canfirtina committed Jul 4, 2023
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13 changes: 11 additions & 2 deletions README.md
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Expand Up @@ -162,13 +162,22 @@ To cite RawHash, you can use the following BibTeX:
```bibtex
@article{firtina_rawhash_2023,
title = {{RawHash}: {Enabling} {Fast} and {Accurate} {Real}-{Time} {Analysis} of {Raw} {Nanopore} {Signals} for {Large} {Genomes}},
doi = {10.1093/bioinformatics/btad272},
author = {Firtina, Can and Mansouri Ghiasi, Nika and Lindegger, Joel and Singh, Gagandeep and Cavlak, Meryem Banu and Mao, Haiyu and Mutlu, Onur},
journal = {Bioinformatics},
author = {Firtina, Can and Ghiasi, Nika Mansouri and Lindegger, Joel and Singh, Gagandeep and Cavlak, Meryem Banu and Mao, Haiyu and Mutlu, Onur},
volume = {39},
number = {Supplement_1},
pages = {i297-i307},
year = {2023},
month = jun,
year = {2023},
doi = {10.1093/bioinformatics/btad272},
issn = {1367-4811},
url = {https://doi.org/10.1093/bioinformatics/btad272},
}
```

# Acknowledgement

RawHash uses [klib](https://github.com/attractivechaos/klib), some code snippets from [Minimap2](https://github.com/lh3/minimap2) (e.g., pipelining, hash table usage) and [Sigmap](https://github.com/haowenz/sigmap) (e.g., chaining).

We thank [Melina Soysal](https://github.com/melina2200) and [Marie-Louise Dugua](https://github.com/MarieSarahLouise) for their feedback to improve the RawHash implementation and test scripts.
7 changes: 6 additions & 1 deletion test/README.md
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Expand Up @@ -35,11 +35,16 @@ mkdir -p rawhash-env/bin && cd rawhash-env

#Optional Step 0 Creating a conda environment (Note we highly recommend using conda for easy installation of dependencies).
#If not using conda, the packages with the specified versions below (e.g., python=3.6.15) must be installed manually in your environment
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

conda create -n rawhash-env python=3.6.15 pip=20.2.3 ont_vbz_hdf_plugin=1.0.1
conda activate rawhash-env

#Installing SRA Toolkit
wget -qO- https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz | tar xzv; cp -r ./sratoolkit.3.0.1-ubuntu64/bin/* bin/; rm -rf sratoolkit.3.0.1-ubuntu64
wget -qO- https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.1/sratoolkit.3.0.1-ubuntu64.tar.gz | tar xzv; cp -r ./sratoolkit.3.0.1-ubuntu64/bin/* bin/; rm -rf sratoolkit.3.0.1-ubuntu64

#Step 1 Compiling the tools
#Cloning and compiling RawHash
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