software.html

---
layout: default
title:  'Gymrek Lab - Resources'
---

<h4>Check out our lab <a href="https://github.com/gymreklab" target="_blank">github page</a> for more info on our software projects.</h4>

<h2>Tools for analyzing short tandem repeat variation</h2>
<table class="softwaretable" border="1">
  <tbody>
    <tr>
      <td width=50%>
	<h2>GangSTR</h2>
	GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over lobSTR and HipSTR is that it can handle repeats that are longer than the read length.
	<br>
	[<a href="https://pubmed.ncbi.nlm.nih.gov/31194863/" target="_blank">paper</a>]
	[<a href="https://github.com/gymreklab/gangstr" target="_blank">github</a>]
      </td>
      <td width=50%>
	<h2>TRTools</h2>
	TRTools contains a variety of utilities for working with TR genotype files generated by HipSTR, GangSTR, and other repeat genotypers. These include:
	<ul>
	  <li>DumpSTR: a tool for filtering TR VCF files</li>
	  <li>MergeSTR: a tool for merging TR VCF files</li>
	  <li>StatSTR: a tool for computing stats such as allele frequencies from TR VCF files</li>
	  <li>compareSTR: a tool for two TR VCF files</li>
	  <li>qcSTR: a tool for generating various QC plots and metrics on TR VCF files</li>
	</ul>
	<br>
	[<a href="https://pubmed.ncbi.nlm.nih.gov/32805020/" target="_blank">paper</a>]
	[<a href="https://github.com/gymreklab/TRTools" target="_blank">github</a>]
      </td>
    </tr>
    <tr>
      <td width=50%>
	<h2>WebSTR</h2>
	WebSTR (<a href="http://webstr.gymreklab.com">webstr.gymreklab.com</a>) is a web application for browsing a variety of STR datasets. It is based off of the popular ExAC browser.
	<br>
	[<a href="http://webstr.gymreklab.com" target="_blank">WebSTR</a>]
	[<a href="https://github.com/gymreklab/dbstr" target="_blank">github</a>]
      </td>
      <td width=50%>
	<h2>MonSTR</h2>
	MonSTR is a tool for calling de novo mutations from HipSTR or GangSTR VCF files.)
	<br>
  [<a href="https://pubmed.ncbi.nlm.nih.gov/33442040/" target="_blank">paper</a>]
	[<a href="https://github.com/gymreklab/strdenovotools" target="_blank">github</a>]
      </td>

    </tr>

</tbody>
</table>