Description

Known Issues of T2T-CHM13v2.0 from v2.0_issues.bed

Methods

This file contains regions with low coverage support and locatoin of each error k-mer obtained from HiFi and ONT platforms.

Reads were aligned with Winnowmap 2.01.

Primary read alignments have been processed with asset commit ver. 0133f268eebf308a1c3eb356b564550526465157, and regions meeting the following criteria are reported in each platform:

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

    Additionally, regions below were included:

  • Regions with base error were detected with 21-mers from Illumina-HiFi reads using Merqury
  • Chimeric consensus of two haplotypes and collapsed simple tandem repeat, found from variant calling and other methods

    Raw low coverage tracks from each platform (containing clippings and low coverage from sequencing biases):

  • hifi.pri.issues.bed
  • ont.pri.len1k_idy85.issues.bed

    Display Conventions and Configuration

  •     - Error_Kmer : K-mers found only in the assembly, and not in the Illumina-HiFi hybrid kmer set
  •     - Chimeric_Hap (Joined two haplotypes) or Collapse
  •     - Low (Low coverage) or Low_Qual : Low coverage associated with consensus error
  •     - Inversion breakpoint error at P5 palindrome and a likely assembly error in the Y chromosome

    Data access

  • https://github.com/marbl/CHM13-issues/v1.0_issues.bed
  • https://github.com/marbl/CHM13-issues/v1.1_issues.bed
  • https://github.com/marbl/CHM13-issues/v2.0_issues.bed

    Release history

    1. 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
    2. 2021 Jun 24. Update to include error k-mers, removing clippings and calls from sequencing biases
    3. 2021 Apr 28. Internal release
    4. 2021 Feb 23. Internal release

    Contacts

    Credits

    Please cite the following papers:

  • Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods 19, 687–695 (2022). https://doi.org/10.1038/s41592-022-01440-3
  • Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ et al. The complete sequence of a human Y chromosome. Nature 621, 344–354 (2023). https://doi.org/10.1038/s41586-023-06457-y