Assembly evaluation with quast
As usual, we are going to use quast for assembly evaluation:
cd ~/workdir
quast.py -t 14 -o ~/workdir/quast_pilon -R ~/workdir/data/Reference.fna ~/workdir/assembly/assembly.fasta ~/workdir/pilon/pilon_round1.fasta ~/workdir/pilon/pilon_round2.fasta ~/workdir/pilon/pilon_round3.fasta ~/workdir/pilon/pilon_round4.fasta
QUAST generates HTML reports including a number of interactive graphics. To access these reports, open a file browser.