WGS Assembly evaluation with QUAST(2)¶
We run:
quast.py
with the following parameters:
| What? | parameter | Our value |
|---|---|---|
| The input assembly | positional | ~/workdir/assembly/assembly_wgs/assembly.contigs.fasta/ |
| The output directory | -o | ~/workdir/assembly/assembly_wgs/quast/ |
| The number of threads to be used | -t | 14 |
The complete commandline is:
quast.py -t 14 -o ~/workdir/assembly/assembly_wgs/quast/ -r ~/workdir/wuhan.fasta ~/workdir/assembly/assembly_wgs/assembly.contigs.fasta
QUAST generates HTML reports including a number of interactive graphics. To access these reports, open them using a file browser:
firefox ~/workdir/assembly/assembly_wgs/quast/report.html
Inspect the results - are you satisfied with the assembly now?