Question: whole genome sequence of GM12878 and K562
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gravatar for f68
2.0 years ago by
f680
f680 wrote:

Hi everybody, I am looking for whole genome sequence of GM12878 and K562 but cannot find them. Any help pointing to the place where I can download it would be greatly appreciated.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by f680
1

Illumina has a boatload of NA12878 raw sequence data (from NovaSeq and other sequencers) available in public data section of BaseSpace.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax78k

If you want assembled, annotated genomes, I don't think they exist (but maybe there is an assembled genome for K562, see this pre-print). You can get sequence data, see here and here for pointers.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by h.mon29k
2
gravatar for colindaven
2.0 years ago by
colindaven2.0k
Hannover Medical School
colindaven2.0k wrote:

If I am not wrong, GM12878 is one of the trio listed here:

https://github.com/PacificBiosciences/DevNet/wiki/Datasets

Someone will have assembled it all somewhere, I am sure you can find a preprint or find it in NCBI.

ADD COMMENTlink written 2.0 years ago by colindaven2.0k
0
gravatar for f68
2.0 years ago by
f680
f680 wrote:

Searching for NA12878 (instead of GM12878) returned sequence from 1000 Genome Project.

ADD COMMENTlink written 2.0 years ago by f680
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