In the ideal case, we have available reference genome we can use to evaluate how correct our assembly is. Very straightforward tool that allows integrated comparison of multiple assemblies to known reference is called quast.

Another option would be to align the assembly to reference using one of the whole genome aligning tools like Mumer, LAST or Minimap2.

Quast

If you have your own assembly, just get this reference, otherwise you can also download assemblies from shared directory.

mkdir ~/reference
cd ~/reference
wget ftp://ftpmrr.unil.ch/LongReadWorkshop/data/dmel_ch4_reference.fasta.gz

To run quast withing this docker image you will need to run it with root access (sudo)

sudo quast.py -o <name of output dir>
  -R <path to reference genome>
  <path to Canu assembly>
  <path to Miniasm assembly>

This command will produce a decent overview of differences between genome assemblies.

Next

Read about Continuity metrics .

Read about Completeness metrics .

Read about Contamination .

Finish this section, go to Checkpoint

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