how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?

assembly levels can be improved using few steps but is there any specific protocol for it ?

To obtain a complete genome assembly from contigs, you need to perform scaffolding, gap filling, and polishing. Here’s an overview of the steps involved:

Scaffolding: Scaffolding is the process of linking contigs together into larger sequences (scaffolds) using additional information such as long-read or paired-end sequencing data. Scaffolding can help to increase the size of the contigs and improve the accuracy of the assembly.

Gap filling: After scaffolding, there may still be gaps between the contigs that need to be filled. This can be done using PCR, Sanger sequencing, or long-read sequencing technologies such as PacBio or Oxford Nanopore. Gap filling can help to improve the continuity and accuracy of the assembly.

Polishing: After scaffolding and gap filling, the assembly can be polished to improve its accuracy. This involves correcting errors in the assembly, such as mismatches, indels, and base-call errors. This can be done using tools such as Pilon or Racon, which use the high-quality reads to correct the errors in the assembly.

Evaluation: Finally, the assembly should be evaluated to assess its quality. Metrics such as N50, genome completeness, and accuracy should be calculated to ensure that the assembly meets the desired standards.

It is important to note that obtaining a complete genome assembly can be a challenging task, and the quality of the assembly depends on the quality and quantity of the sequencing data, the choice of assembly algorithm, and the quality of the scaffolding, gap filling, and polishing steps. Therefore, it is important to carefully evaluate the assembly at each step to ensure that it is of high quality.

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