QUAST is a state-of-the-art tool for (meta)genome assembly evaluation, computing over 50 quality metrics and presenting results in plain text, static plots, and interactive HTML reports.
The current QUAST toolkit includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, QUAST-LG, the extension for large genomes (e.g., mammalians), and Icarus, the interactive visualizer for these tools.
The QUAST package works with and without reference genomes. However, it is much more informative if at least a close reference genome is provided along with the assemblies. The tool accepts multiple assemblies and is thus suitable for comparison.
This description gives a snapshot of the QUAST running instructions, output interpretation, and reported quality metrics. The online manual provides a much more detailed description of these and many other topics.
QUAST requires a 64-bit Linux or macOS machine with Python 3. The basic running command is below.
./quast.py test_data/contigs_1.fasta \
test_data/contigs_2.fasta \
-r test_data/reference.fasta.gz \
-g test_data/genes.txt \
-1 test_data/reads1.fastq.gz -2 test_data/reads2.fastq.gz \
-o quast_test_output
report.txt summary table
report.tsv tab-separated version, for parsing, or for spreadsheets (Google Docs, Excel, etc)
report.tex Latex version
report.pdf PDF version, includes all tables and plots for some statistics
report.html everything in an interactive HTML file
icarus.html Icarus main menu with links to interactive viewers
contigs_reports/ [only if a reference genome is provided]
misassemblies_report detailed report on misassemblies
unaligned_report detailed report on unaligned and partially unaligned contigs
k_mer_stats/ [only if --k-mer-stats is specified]
kmers_report detailed report on k-mer-based metrics
reads_stats/ [only if reads are provided]
reads_report detailed report on mapped reads statistics