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Genome Assembly

Introduction:

Viral genome assembly from sequenced reads and identification of variants along the genome.

Whole-genome sequencing (WGS) of pathogens is gaining vital significance, encompassing basic research and extending its reach into clinical science and practice. Within the field of virology, WGS plays a key role in advancing novel treatments and vaccines while simultaneously supplementing the capabilities of molecular epidemiology and evolutionary genomics.


Next-Generation Sequencing (NGS) Quality Control and Alignment:

Data quality assessment begin with FastQC. Adapters and low-quality 3' regions are removed from the reads using Fastp. Alignment was performed against the KRAKEN2 database, where reads are mapped to the Homo sapiens genome. The remained reads are used for downstream analysis.


Separation of Host and Viral Reads:

Unclassified, trimmed reads underwent assembly using the Spades assembly toolkit, resulting in scaffolds. These scaffolds were aligned with the submitted viral genome (AF077761.1) using BLASTN to identify positions and alignments within the reference genome precisely.


Closing the Gaps and Comparative Analysis:

Gaps in the assembly were addressed using ABACAS, involving a comparison between the assembled scaffolds and the reference genome to bridge any discontinuities. The refined assembly underwent evaluation using QUAST to generate an assembly report.


Visualization:

Finally, the assembled genome was visualized using PlasmidID, clearly representing the modified viral genome's structural characteristics.

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