Question

Does anyone know where I can get whole genome sequence eukaryotic trio FASTA files?

0

Entering edit mode

4.3 years ago

screadore ▴ 20

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 • 878 views

ADD COMMENT • link 4.3 years ago by screadore ▴ 20

1

Entering edit mode

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

ADD REPLY • link 4.3 years ago by GenoMax 147k

0

Entering edit mode

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

ADD REPLY • link 4.3 years ago by screadore ▴ 20

1

Entering edit mode

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

ADD REPLY • link 4.3 years ago by GenoMax 147k

0

Entering edit mode

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

ADD REPLY • link 4.3 years ago by screadore ▴ 20

1

Entering edit mode

Follow the workflow described here.

ADD REPLY • link 4.3 years ago by GenoMax 147k

score 1 · Answer 1 · 2020-07-27

1

Entering edit mode

4.3 years ago

JC 13k

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 COMMENT • link 4.3 years ago by JC 13k