---
layout: page
title: Download
permalink: /download/
order: 5
share: false
---

Please cite:  
>Kim, D., Paggi, J.M., Park, C. _et al._ Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. _Nat Biotechnol_ **37**, 907–915 (2019). <https://doi.org/10.1038/s41587-019-0201-4>

- TOC
{:toc}

## Index
HISAT2 indexes are hosted on AWS (Amazon Web Services), thanks to the AWS Public Datasets program. Click this [link](https://registry.opendata.aws/jhu-indexes/) for more details.

{% for item in site.data.download-index %}
### {{ item.organism }}
  {% for data in item.data %}
<li>{{ data[0] }}</li>
<table style="border-collapse: collapse; border: none;">
{% for genome in data[1] %}
<tr style="border: none;"><td style="border: none;">{{ genome[0] }}</td>
  <td style="border: none;">
  {% for url in genome[1] %}
  <a href="{{ url[1] }}">{{ url[1] }}</a><br/>
  {% endfor %}
  </td>
</tr>
{% endfor %}
</table>
{% endfor %}
{% endfor %}


    genome: HISAT2 index for reference
    genome_snp: HISAT2 Graph index for reference plus SNPs
    genome_tran: HISAT2 Graph index for reference plus transcripts
    genome_snp_tran: HISAT2 Graph index for reference plus SNPs and transcripts


## Binaries
{: binaries }

{% assign targets = site.data.download-binary.latest_version | split: "," %}
{% for release in site.data.download-binary.release %}
{% assign version = release['version'] %}
{% if targets contains version or targets == null %}
{% assign name = release['name'] %}
### Version: {{name}} {{version}}
<table style="border-collapse: collapse; border: none;">
<tr style="border: none;"><td style="border: none;" colspan="2"><b>Release Date</b>: {{release['date']}}</td></tr>
{% for artifact in release['artifacts'] %}
{% assign type = artifact[0] %}
<tr style="border: none;"><td style="border: none;">{{type}}</td><td style="border: none;"><a href="{{artifact[1]}}">{{artifact[1]}}</a></td></tr>
{% endfor %}
</table>
{% endif %}
{% endfor %}

