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Understanding the quality of your genome reference sequence and knowing how to assemble high-quality genomes are core bioinformatics skills. So far, we have learned a great deal about variant calling and alignment, as well as gene annotation. The quality of these steps is greatly impacted by the underlying reference genome. As you might imagine, variants cannot be mapped effectively to poorly assembled regions, and genes cannot be called well when you have incorrect bases or other issues in your assembly.In the past few years, there have been tremendous advances in genome sequencing and assembly that have transformed the field. In this chapter, we’ll learn about how those advances have impacted bioinformatics and the resulting benefits.In this chapter, we will cover:
- Accessing genome assemblies
- Working with graph genomes
- Long-read assembly with Raven
- Assessing genome quality with QUAST
