MetaQUAST

QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. You can find all project news and the latest version of the tool at sourceforge. QUAST utilizes MUMmer, GeneMarkS, GeneMark-ES, GlimmerHMM, and GAGE. In addition, MetaQUAST uses MetaGeneMark, Krona tools, BLAST, and SILVA 16S rRNA database. See the metaQuast home page for more info.

In case not all assemblies finished so far, copy the pre-computed assembly results to your local directory:

cd /mnt/WGS-data
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/denbi-mg-course/assembly_results.tar
tar xvf assembly_results.tar
cp -v -r /mnt/WGS-data/assembly_results/* .

To call metaquast.py we have to provide reference genomes which are used to calculate a number of different metrics for evaluation of the assembly. In real-world metagenomics, these references are usually not available, of course:

cd /mnt/WGS-data

metaquast.py --threads 14 --gene-finding \
-R /mnt/WGS-data/genomes/Aquifex_aeolicus_VF5.fna,\
/mnt/WGS-data/genomes/Bdellovibrio_bacteriovorus_HD100.fna,\
/mnt/WGS-data/genomes/Chlamydia_psittaci_MN.fna,\
/mnt/WGS-data/genomes/Chlamydophila_pneumoniae_CWL029.fna,\
/mnt/WGS-data/genomes/Chlamydophila_pneumoniae_J138.fna,\
/mnt/WGS-data/genomes/Chlamydophila_pneumoniae_LPCoLN.fna,\
/mnt/WGS-data/genomes/Chlamydophila_pneumoniae_TW_183.fna,\
/mnt/WGS-data/genomes/Chlamydophila_psittaci_C19_98.fna,\
/mnt/WGS-data/genomes/Finegoldia_magna_ATCC_29328.fna,\
/mnt/WGS-data/genomes/Fusobacterium_nucleatum_ATCC_25586.fna,\
/mnt/WGS-data/genomes/Helicobacter_pylori_26695.fna,\
/mnt/WGS-data/genomes/Lawsonia_intracellularis_PHE_MN1_00.fna,\
/mnt/WGS-data/genomes/Mycobacterium_leprae_TN.fna,\
/mnt/WGS-data/genomes/Porphyromonas_gingivalis_W83.fna,\
/mnt/WGS-data/genomes/Wigglesworthia_glossinidia.fna \
-o quast \
-l MegaHit,metaSPAdes,Ray_31,Ray_51,velvet_31,velvet_51,idba_ud \
megahit_out/final.contigs.fa \
metaspades_out/contigs.fasta \
ray_31/Contigs.fasta \
ray_51/Contigs.fasta \
velvet_31/contigs.fa \
velvet_51/contigs.fa \
idba_ud_out/contig.fa

QUAST generates HTML reports including a number of interactive graphics. To access these reports, load the reports in your web browser:

firefox quast/report.html