CHM13-issues
December 2, 2022 ยท View on GitHub
CHM13 human reference genome issue tracking
For any downstream analysis, please use the following files:
- Possible consensus or mis-assembly issue: <ver.>_issues.bed
- Het sites: <ver.>/chm13.draft_<ver.>.curated_sv.20210612.vcf, <ver.>/chm13.draft_<ver.>.hets_combined.20210615.bed
Releases
- 2022-12-02 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
- 2021-10-13 Het regions lifted over from v1.0 to v1.1
- 2021-06-23 Updating 3 additional issues and adding error k-mers in v1.0 and v1.1
- 2021-06-15 Validated het SVs and clusters of heterozygous sites in v1.0 assembly
- 2021-04-28 Issues track for HiFi and ONT read alignments from Winnowmap 2.01
- 2021-03-08 Combined low coverage and clipped regions
- 2021-02-23 Low coverage regions for HiFi, CLR, and ONT read alignments
Issues.bed file format
| Label | Description | R,G,B | Color |
|---|---|---|---|
| Low | Low coverage | 204,0,0 | red |
| Low_Qual | Low coverage from lower consensus quality | 204,0,0 | red |
| Error_Kmer | K-mers identified as errors from the Illumina-HiFi hybrid 21-mers | 0,0,0 | black |
| Collapse | Approximate region conatining sequence collapse | 204,0,0 | red |
| Chimeric_Hap | Chimeric consensus of two haplotypes | 204,0,0 | red |
Methods
Brief descriptions are provided for
More details for the polishing and evaluation methods applied on CHM13 is available in T2T-Polish. For the methods used for polishing a nd evaluating the Y, see this preprint for more details.
Citation
Please cite the papers below if any of the materials posted on this github are used:
- Issues found in HG002XYv2.7, especially the Y: Rhie A, Nurk S, Cechova M, Hoyt S, Taylor DJ et al., The complete sequence of a human Y chromosome. bioRxiv (2022) https://doi.org/10.1101/2022.12.01.518724
- General methods for finding issues and hets: Mc Cartney AM, Shafin K, Alonge M et al., Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods (2022) https://doi.org/10.1038/s41592-022-01440-3 (bioRxiv version: https://doi.org/10.1101/2021.07.02.450803)
- Issues for v0.9-v1.1: Nurk S, Koren S, Rhie A, and Rautiainen M et al., The complete sequence of a human genome. Science (2022) https://doi.org/10.1126/science.abj6987