Possibility of using 10x Genomics reads from another individual
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13 months ago

Hi Everybody, I am trying to assemble a genome of an animal species. We used the long reads (HiFi) to obtain the first draft. We also have 10x reads but from another individual. I am wondering if I could use 10x genomics reads to scaffold the first draft assembly, is it possible or can it affect the accuracy of assembly?

genome-assembly • 461 views
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10x genomic reads were useful to create smaller localized assemblies using linked read information. That kit has since been discontinued by 10x so I don't know how you are planning to use the 10x data. If you simply add them to your other data then they would just be plain illumina reads without any added significance. You could use longranger to use the linked read feature but then you would need to reconcile this assembly with whatever else you have.

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I have generated an assembly draft using PacBio reads. Now, I want to integrate linked 10x reads to the first draft using scaff10x pipeline. It can improve the assembly a bit but I wonder if the output is accurate because the origin of linked 10x reads and pacbio reads are from different individuals.

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are from different individuals

If you are working with in-bred animals then this likely won't be an issue. Are you simply looking to improve the assembly? Perhaps comparing assemblies coming out of longranger with yours should give you an idea of what to expect? I am thinking out aloud here.