Eukaryotes: De Novo Genome Assembly and Annotation

Step 1 - Assess quality of sequenced reads

Step 2 - Preprocess raw data

• Adapter removal
• Trimming

Step 3 - Genome assembly

• Short reads assembly with de Bruijn assemblers
• Long reads genome assembly
• Need long reads correction due to high rates of sequence errors
• Need more sequence coverage (~50x)

Step 4 - Assembly evaluation

• Compare assemblies, pick one with highest percentage of complete genes

Step 5 - Scaffolding and gap filling

• Remove repetitive contigs
• Build scaffolds with longest contigs
• Close large number of gaps

Step 6 - Compare assembly metrics

• Total number of contigs in assembly
• Largest contig
• Total number of bases in assembly
• Number of misassembled contigs
• Misassembled contigs length

Step 7 - Gene prediction

• Predict novel genes
• Final consensus gene models

Step 8 - functional annotation

• Identify differentially expressed genes
• Annotate gene
• GO terms
• KEGG Pathways