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maiziex / Aquila

Diploid personal genome assembly and comprehensive variant detection based on linked-reads
MIT License
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Aquila for non-model insect genomes #3

Open hanclair opened 2 years ago

hanclair commented 2 years ago

Hi, I am wondering if Aquila is applicable to genomes from non-model insect species, or is it meant only for human genomes? Assuming I can generate uniqueness map for the reference of my non-model species, are there any additional steps in the Aquila pipeline that are human genome specific?

I am wondering this because of the option to use variant calls from the 1000 Genomes Project to partition reads between haplotypes, the comment about chrX vs chr23, and the ground truth calls seem to be all from human data. "We now have a new version for step1 to use 1000 Genomes VCF as the input VCF file (please check here), and Aquila will use common variants from 1000G to help partition linked-reads".

Thank you very much.

Sincerely, Clair

maiziex commented 2 years ago

Hi Clair, You are right, Aquila is used for the human genome or non-human primate genome right now. For the diploid genome with a high-quality draft reference, you can still use it.

Best Maizie