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Telomere-to-Telomere diploid Indian Genome

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

Assembly release

v0.4

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.

v0.2

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

  1. 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.

  2. https://github.com/arangrhie/T2T-Polish/tree/master/merqury

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Telomere-to-Telomere diploid Indian Genome

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