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 /vol/spool/tutorial-data
python ~/quast-3.1/metaquast.py --threads 16 --gene-finding --meta \
-R /vol/spool/tutorial-data/genomes/Aquifex_aeolicus_VF5.fna,\
/vol/spool/tutorial-data/genomes/Bdellovibrio_bacteriovorus_HD100.fna,\
/vol/spool/tutorial-data/genomes/Chlamydia_psittaci_MN.fna,\
/vol/spool/tutorial-data/genomes/Chlamydophila_pneumoniae_CWL029.fna,\
/vol/spool/tutorial-data/genomes/Chlamydophila_pneumoniae_J138.fna,\
/vol/spool/tutorial-data/genomes/Chlamydophila_pneumoniae_LPCoLN.fna,\
/vol/spool/tutorial-data/genomes/Chlamydophila_pneumoniae_TW_183.fna,\
/vol/spool/tutorial-data/genomes/Chlamydophila_psittaci_C19_98.fna,\
/vol/spool/tutorial-data/genomes/Finegoldia_magna_ATCC_29328.fna,\
/vol/spool/tutorial-data/genomes/Fusobacterium_nucleatum_ATCC_25586.fna,\
/vol/spool/tutorial-data/genomes/Helicobacter_pylori_26695.fna,\
/vol/spool/tutorial-data/genomes/Lawsonia_intracellularis_PHE_MN1_00.fna,\
/vol/spool/tutorial-data/genomes/Mycobacterium_leprae_TN.fna,\
/vol/spool/tutorial-data/genomes/Porphyromonas_gingivalis_W83.fna,\
/vol/spool/tutorial-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. To access these reports, copy the quast directory to your public_html folder:

cp -r quast ~/public_html

After that, you can load the reports in your web browser:

http://YOUR_AWS_IP/~ubuntu/quast/summary/report.html
http://YOUR_AWS_IP/~ubuntu/quast/combined_quast_output/report.html