—- we ended up not using this page but that one instead https://docs.google.com/document/d/1cV2aX6_f8-BlabJ44vK6V0sPg1fOpLSW9z8fNFQAuXM/edit?ts=5e182389
Expected learning outcome
The objective of this activity is to have some flavor of metagenomics assembly. You will see, this is a really lightweight lab.
Part 1 out of 1: the whole lab
An assembly made using short and long reads and the MEGAHIT assembler is provided.
Run Metaquast to evaluate its quality:
metaquast.py --min-identity 90. --ambiguity-usage all -R refs -t 4 --debug -o metaquast illumina/megahit_0p1/final.contigs.fa
Use a tool provided with MEGAHIT to obtain the assembly graph (in FASTG format):
megahit_core contig2fastg 141 illumina/megahit_0p1/intermediate_contigs/k141.contigs.fa > k141.fastg
Use Bandage to convert the FASTG format (assembly graph) into the GFA format (another more popular assembly graph format), then visualize it.
Bandage reduce k141.fastg k141.gfa Bandage image k141.gfa k141.png mimeopen k141.png
What do you observe?
How is it different from the assembly graphs you visualized two days ago in the genome assembly lecture?