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Today, I will talk to you about how to use hi-C data to assist in the assembly of Aedes aegypti genomes. Many people may not know much about it. In order to make you understand better, the editor has summarized the following for you. I hope you can get something from this article.

As early as 2013, some scientists have put forward the idea of using Hi-C data to assist genome assembly, which can further enhance the length of scaffold to the chromosome level, and provide a supporting analysis software LACHESIS. The result of genome assembly entered by the software by default is completely correct, and the subsequent operations are based on this premise. However, in practice, due to the limitation of the assembly algorithm, there will be splicing errors in the genome sketch.

Analysis idea: first, according to the results of hi-c data, the splicing errors in the input genome assembly results are corrected, and then the subsequent analysis is carried out. The whole pipeline is shown in the following figure.

It can be divided into the following four major steps

Preliminary filtration

Misjoin correction

Ordering and orientation

Overlap merging

The first step is to preprocess the results of genome assembly to remove scafflod that is too short in length. If the length of scaffold is too short, the corresponding interactive information in hi-c atlas will be very little, and the subsequent analysis cannot be carried out effectively without enough interactive information. The second step is to use hi-c data to correct splicing errors in scaffold. For scaffold detected with splicing errors, cut it into inconsistent parts with splicing errors and consistent parts without splicing errors, inconsistent part will not carry out follow-up analysis.

The third step is to determine the scaffold belonging to the same chromosome, and to sequence and adjust the direction; the fourth step is to detect whether there is overlap between the scaffold on the same chromosome, and merge for the scaffold with overlap.

After reassembling the genome of Aedes aegypti using this algorithm combined with hi-c data, the results are as follows.

As you can see, the original sketch is assembled to the final chromosome level. This algorithm is suitable for any genome assembly. It is worth mentioning that in the final results of genome assembly assisted by hi-c data, there will still be some wrong results, which is inevitable.

After reading the above, do you have any further understanding of how to use hi-C data to assist in the assembly of Aedes aegypti genome? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

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