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maiziex / Aquila

Diploid personal genome assembly and comprehensive variant detection based on linked-reads
MIT License
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Minimum coverage requirement #6

Open pontushojer opened 1 year ago

pontushojer commented 1 year ago

Does Aquila have a minimal coverage requirement? Would it be feasible to run on say a 30X coverage dataset?

maiziex commented 1 year ago

there is no coverage requirement, 30x coverage is adequate.

pontushojer commented 1 year ago

Thanks for the quick answer!

Have you check the affect of lower coverage? In your paper it seems the lowest tested was about 78X which is still quite deep. Closer to assembly coverage than what you would need for straight variant calling anyway. I imagine it is harder for Aquila to assemble the full haplotypes with significantly lower coverage.

maiziex commented 1 year ago

In the paper, most of the datasets are customized libraries, and we also test some public datasets and subsampled datasets. 30x should be fine.