Question

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

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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 • 882 views

ADD COMMENT • link 4.3 years ago by screadore ▴ 20

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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

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

ADD REPLY • link 4.3 years ago by screadore ▴ 20

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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

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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

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Follow the workflow described here.

ADD REPLY • link 4.3 years ago by GenoMax 147k

score 1 · Answer 1 · 2020-07-27

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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