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This GFA file can be visualized by graph visualization programs like Bandage [8]. The

Bandage program is available at “http://rrwick.github.io/Bandage/” and can be down-

loaded and installed on Linux, Windows, and Mac OX. Visualizing a graph file will give

you an idea about the assembly quality. You can zoom in and out and do many operations

on the graph file. Moreover, there are good graph visualization packages in Python and R

such as igraph [9], which is available in both programming platforms. To read more about

Bandage and igraph, refer to their user manuals which are available on their web pages.

8.2.5  Assembly Evaluation

MetaSPAdes produced several assemblies for different species in a single scaffolds file.

Those assemblies can be evaluated by using an evaluation program like “metaquast.py”

[10], which is a Python-based program that can generate report showing the quality of the

assemblies. For the installation instructions of this program, visit “http://cab.cc.spbu.ru/

quast/manual.html”. To generate report for the scaffolds for each of the three samples, you

can run the following:

metaquast.py -t 4 \

-m 500 \

metag_healthy/scaffolds.fasta \

metag_moderate/scaffolds.fasta \

metag_severe/scaffolds.fasta \

-o output

This will generate an HTML report in the “output” directory. The other directories and

files are linked to this report when it is displayed on the Internet browser. You can display

“report.html” file by using “firefox report.html”.

FIGURE 8.3  Graphic Fragment Assembly (GFA) file format.