Question: Retrieving Individual Genomes From 1000Genomes Project
1
gravatar for Alper Yilmaz
6.0 years ago by
Alper Yilmaz90
Turkey
Alper Yilmaz90 wrote:

Hi all.. I was interested in retrieving individual genomes as fasta files from 1000genomes project. After some search I noticed that, the reference genome is available, individual sequencing reads (fastq format) are available, variant calls are available but individual assembled genomes are not available (or I couldn't find it). So, is it possible to locate individual genome files? Are they provided to public? I'm guessing that individual genomes might not be available due to privacy considerations..

thanks..

genome 1000genomes • 1.5k views
ADD COMMENTlink modified 6.0 years ago by zam.iqbal.genome1.7k • written 6.0 years ago by Alper Yilmaz90
3
gravatar for zam.iqbal.genome
6.0 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

There is no privacy issue, but there was never any intention of trying to assemble (meaning making a haploid consensus) of each sample. The experimental design is low coverage on many samples (too low to do an individual assembly), with the goal of finding the majority of variation. So as Pierre says, the "main" product is a set of VCFs

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by zam.iqbal.genome1.7k
1
gravatar for Pierre Lindenbaum
6.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

there is no assembly for the sequenced individuals, bit their variations are available: e.g:ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804

ADD COMMENTlink written 6.0 years ago by Pierre Lindenbaum118k
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