Quast_2.rst

Assembly evaluation with QUAST(2) ==============================

We run:

quast.py

with the following parameters:

+------------------------------------------+-------------------------+--------------------------------------------------------------------+ | What? | parameter | Our value | +==========================================+=========================+====================================================================+ | The input assembly | positional | ~/workdir/assembly/small_assembly/assembly.contigs.fasta/ | +------------------------------------------+-------------------------+--------------------------------------------------------------------+ | The output directory | -o | ~/workdir/assembly/small_assembly/quast/ | +------------------------------------------+-------------------------+--------------------------------------------------------------------+ | The number of threads to be used | -t | 14 | +------------------------------------------+-------------------------+-------------------------------------------numb-------------------------+ | The reference genome used | -r | ~/workdir/wuhan.fasta | +------------------------------------------+-------------------------+--------------------------------------------------------------------+

The complete commandline is:

quast.py -t 14 -o ~/workdir/assembly/small_assembly/quast/ -r ~/workdir/wuhan.fasta ~/workdir/assembly/small_assembly/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/small_assembly/quast/report.html

Inspect the results - are you satisfied with the assembly?

References

quast http://sourceforge.net/projects/quast