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 QUAST home page for more info.

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 ~/workdir/assembly

qsub -cwd -pe multislot 24 -N metaquast -l mtc=1 -b y \
/vol/cmg/bin/metaquast.py --threads 24 --gene-finding --meta \
-R /vol/metagencourse/DATA/WGS-data/genomes/Aquifex_aeolicus_VF5.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Bdellovibrio_bacteriovorus_HD100.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydia_psittaci_MN.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydophila_pneumoniae_CWL029.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydophila_pneumoniae_J138.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydophila_pneumoniae_LPCoLN.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydophila_pneumoniae_TW_183.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Chlamydophila_psittaci_C19_98.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Finegoldia_magna_ATCC_29328.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Fusobacterium_nucleatum_ATCC_25586.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Helicobacter_pylori_26695.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Lawsonia_intracellularis_PHE_MN1_00.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Mycobacterium_leprae_TN.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Porphyromonas_gingivalis_W83.fna,\
/vol/metagencourse/DATA/WGS-data/genomes/Wigglesworthia_glossinidia.fna \
-o quast \
-l MegaHit,Ray_31,velvet_31,velvet_51,idba_ud \
megahit_out/final.contigs.fa \
ray_31/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. You can load the reports into your web browser:

firefox quast/summary/report.html
firefox quast/combined_quast_output/report.html