We have sequenced a EBV-immortalized human male cell line from SG10k samples on different platforms. The data contains ~106x of Pacbio HiFi, ~64x of Oxford Nanopore (ONT) Duplex, ~222x ONT Ultralong (ULONT), ~100x MGI WGS short reads, ~33x Illumina WGS short reads and ~120x Omni-C for the child sample (I002C). Statistics of BioNano will be added soon.
For parental samples:
| SampleType | SampleID | HiFi (REVIO) | Duplex | MGI |
|---|---|---|---|---|
| Father | I002A | 60x | 21x | 35x |
| Mother | I002B | 61x | 20x | 37x |
The data statistics are provided in an excel
This assembly version results from performing two rounds of polishing, as outlined in the procedure from 1.
The v0.4 assembly has a improved QV values, with Maternal at 72.35 and Paternal at 70.97. QV values are estimated using hybrid k-mers generated from Pacbio HiFi and MGI WGS data as described in 2. Chromosome wise QV values are listed in an excel file.
This version of the assembly contains Telomere-to-Telomere chromsomes for both maternal and paternal haplotypes including a mitochondria. In this version of the genomes, rDNAs have not been resolved.
| Maternal | Paternal | |
|---|---|---|
| T2T Chromosomes | 23 | 23 |
| Size | 3,022,465,370 | 2,934,829,127 |
| NG50 | 154,891,367 | 146,273,588 |
| %GC | 40.82 | 40.79 |
Assembly files (zipped):
If you wish to download the files using wget, you may use wget -O <haplotype>.fasta.gz <link>
Assembly QV is calculated with yak tool using I002C MGI WGS dataset. Per chromosome QV values are provided in an excel file
Note: The data available on this GitHub page can be accessed either from LHG or LBCB GitHub pages
Footnotes
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Mc Cartney, Ann M., et al. "Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies." Nature methods 19.6 (2022): 687-695. ↩
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https://github.com/arangrhie/T2T-Polish/tree/master/merqury ↩