Genome analysis and improvement
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9 weeks ago
Duminda ▴ 10

Hello all,

I am conducting a mammalian genome analysis. I obtained 76% BUSCO completeness of the first hybrid genome by combining Illumina HiSeq x Ten short-read genome and Nanopore MinIon long-read genome. After hybrid analysis of this with Bionano saphyr seq data.. the second hybrid genome shows 75% BUSCOs and it is not improved as we thought. I appreciate your comments on this... and also request suggestions for further improvement of this genome... I also have transcriptomic data and stLFR seq data...

genome • 589 views
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Perhaps you want to describe what you did to assemble the genome?

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Thank you.. Initially, Illumina and nanopore data were analyzed by LRScaf and produced the first hybrid genome. Then, that genome was used for analysis with Bionano saphyr data and the second hybrid genome was obtained.

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So, Bionano is used only to improve scaffolding so shouldn't impact your BUSCO analysis much (unless correcting for an assembly error), so I think it really comes down to your assembly. How much coverage do you have with the Nanopore reads? perhaps you want to just try assembling a genome with this first? (Followed by a hybrid polishing pipeline)?

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Thank you.. the nanopore coverage was around 6.4X .. I will try it first as you suggested...

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This is rather low coverage for assembly but perhaps it will at least give you an idea of whether the low BUSCO percentage is due to assembly issues.. \ Do you at least see significant improvement in assembly contiguity by adding the nanopore data compared to an illumina only assembly?

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Yes, BUSCO with the only Illumina data gives 58% and so, nanopore gives a significant improvement to the genome...

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