description.html

<h2>Description</h2>
<p>
Known Issues of T2T-CHM13v2.0 from v2.0_issues.bed
</p>

<h2>Methods</h2>
<p>
This file contains regions with low coverage support and locatoin of each error k-mer obtained from HiFi and ONT platforms.<br><br>

Reads were aligned with Winnowmap 2.01.<br><br>
Primary read alignments have been processed with asset commit ver. <code>0133f268eebf308a1c3eb356b564550526465157</code>, and regions meeting the following criteria are reported in each platform:<br>

<li> Less than 7 reads aligned in hifi, 10 reads aligned in ONT<br>
<li> Merged when regions are less than 5 kb apart<br>
<li> Exclude low coverage at both 3 kb ends of each chromosome due to natural coverage drop<br>
<li> Exclude low coverage overlapping rDNA gaps<br><br>

Additionally, regions below were included:<br><br>
  
<li> Regions with base error were detected with 21-mers from Illumina-HiFi reads using Merqury
<li> Chimeric consensus of two haplotypes and collapsed simple tandem repeat, found from variant calling and other methods

</p>
<p>
Raw low coverage tracks from each platform (containing clippings and low coverage from sequencing biases):
<li> hifi.pri.issues.bed
<li> ont.pri.len1k_idy85.issues.bed
</p>
<h2>Display Conventions and Configuration</h2>
<!-- if there are special conventions, like colors, describe them here -->
<p>
<li><span style='border: 1px inset #000000; background-color:#000000;'>&nbsp;&nbsp;&nbsp;</span> - Error_Kmer : K-mers found only in the assembly, and not in the Illumina-HiFi hybrid kmer set
<li><span style='border: 1px inset #000000; background-color:#f00000;'>&nbsp;&nbsp;&nbsp;</span> - Chimeric_Hap (Joined two haplotypes) or Collapse
<li><span style='border: 1px inset #000000; background-color:#f00000;'>&nbsp;&nbsp;&nbsp;</span> - Low (Low coverage) or Low_Qual : Low coverage associated with consensus error
<li><span style='border: 1px inset #000000; background-color:#9999ff;'>&nbsp;&nbsp;&nbsp;</span> - Inversion breakpoint error at P5 palindrome and a likely assembly error in the Y chromosome
</p>


<h2>Data access</h2>
<!-- Optional, links for downloading the data if there is a separate source beside the
browser  -->
<li>https://github.com/marbl/CHM13-issues/v1.0_issues.bed
<li>https://github.com/marbl/CHM13-issues/v1.1_issues.bed
<li>https://github.com/marbl/CHM13-issues/v2.0_issues.bed

<h2>Release history</h2>
<ol>
<li> 2022 Dec 02. Issues added for v2.0. X and Y were simultaneously used in T2T-HG002XYv2.7, and issues found on the Y are appended to v1.1_issues.bed. Note the sequencing data used is from HG002
<li> 2021 Jun 24. Update to include error k-mers, removing clippings and calls from sequencing biases
<li> 2021 Apr 28. Internal release
<li> 2021 Feb 23. Internal release
</ol>

<h2>Contacts</h2>
<ul>
<li><a href="https://github.com/marbl/CHM13-issues">Please report any issues to https://github.com/marbl/CHM13-issues</a>
</ul>
<h2>Credits</h2>
<p>Please cite the following papers:
</p>
<p>
<li>Mc Cartney AM, Shafin K, Alonge M et al. <a href="https://doi.org/10.1038/s41592-022-01440-3">Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies</a>. Nat Methods 19, 687–695 (2022). https://doi.org/10.1038/s41592-022-01440-3
<li>Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ et al. <a href="https://doi.org/10.1038/s41586-023-06457-y">The complete sequence of a human Y chromosome</a>. Nature 621, 344–354 (2023). https://doi.org/10.1038/s41586-023-06457-y
</p>