Question: Does anyone know where I can get whole genome sequence eukaryotic trio FASTA files?
0
gravatar for screadore
4 months ago by
screadore0
screadore0 wrote:

I need the whole genome sequence for a human genome for a trio analysis. I'm trying to test annotation software and can't seem to find a reliable database to get these FASTA files. So any insight would be very insightful. Thank you!

sequencing sequence genome • 170 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by screadore0
1

Sequence/alignment files are available at this GIAB data site. You could generate a consensus based on the alignments provided.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax92k

How do I go about recreating them? Thank you for your insight!

ADD REPLYlink written 4 months ago by screadore0
1

You can also use g2gtools (LINK) along with the VCF files to recreate the custom genomes.

ADD REPLYlink written 4 months ago by genomax92k

Thank you! So if I use g2gtools do you know which command I can use to recreate the custom genomes from the VCF?

ADD REPLYlink written 4 months ago by screadore0
1

Follow the workflow described here.

ADD REPLYlink written 4 months ago by genomax92k
1
gravatar for JC
4 months ago by
JC12k
Mexico
JC12k wrote:

As fasta I believe there are no releases, but Genome in a Bottle can give you the variants from some trios, then you just need to recreate the genome fasta for each one.

ADD COMMENTlink written 4 months ago by JC12k
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