De Novo Genome Assembly    ◾    101

quast.py \

-o quast_Ecoli_ass \

-t 4 \

abyss_ecoli_ass.fasta \

spades_ecoli_ass.fasta \

spades_hyb_ecoli_ass.fasta

If the following error is displayed:

“/home/…/jsontemplate.py” line 583, in <module> ‘html’: cgi.escape,

You may need to open that file “jsontemplate.py” using a text editor of your choice. In

line 50 of that file change “import cgi” to “import html” and in line 583 change “‘html’: cgi.

escape” to “‘html’: html.escape” and rerun the above command.

The above QUAST command saves the output files in “quast_Ecoli_ass” directory. The

assessment report is generated in different formats including pdf, html, text, and TSV. You

can open any of these reports with the right application. We can open “report.html” on

Firefox browser by running the following on the Linux terminal:

cd quast_Ecoli_ass

firefox report.html

This will display a statistics table, which includes assembly assessment statistics (Figure 3.8),

and three interactive plots: cumulative length, Nx, and GC content (two are shown in

FIGURE 3.8  QUAST assembly assessment report.