Assembly

Learning objectives

• Being able to create an assembly with megahit
• Assess the quality of the assembly

Now that our reads are quality trimmed and ready to go is time to start the assembly. We can use megahit:

megahit --12 sample_0.nophix.fastq.gz,sample_1.nophix.fastq.gz,sample_2.nophix.fastq.gz,sample_3.nophix.fastq.gz,sample_4.nophix.fastq.gz,sample_5.nophix.fastq.gz \
        -t 16 \
        -o megahit_assembly_meta \
        --presets meta-sensitive

This command would take around 50 minutes to complete, to speed up things we pre-assembled the data which is available in the precomputed/assembly/ folder.

Feel free to inspect the contents of the folder by using

ls -lh precomputed/assembly/

You will notice the final.contigs.fa file which contains the assembly

Now, we want to find out how well or poorly our assembly went. For this, we use quast, a tool to generate an assembly report.

quast precomputed/assembly/final.contigs.fa -o quast/

Then, we inspect the output from quast.

less quast/report.txt

Not bad! We know our metagenome is not too large and if we care about contiguity, contigs above 5kb represent most of our community