Introduction

This tutorial will orient you to using the QUAST (version 4.0) installed on Atmosphere. This tutorial provides instructions for the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools. 

This tutorial will take users through steps of:

1. Launching the QUAST-4.0 Atmosphere image
2. Running QUAST-4.0 on an test data 

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to upendra@cyverse.org. Thank you.

Part 1: Connect to an instance of an Atmosphere Image (Virtual Machine)

Step 1. Go to https://atmo.iplantcollaborative.org and log in with your CyVerse credentials.

Step 2. Click on the Launch New Instance button and search for QUAST-4.0

Step 3. Select the image QUAST 4.0 and click Launch Instance. It will take 10-15 minutes for the cloud instance to be launched. 

Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs.  This tutorial can be accomplished with the medium instance size, small1 (2 CPUs, 8 GB memory, 60 GB root)

Part 2: Set up a Quast-4.0 run using the Terminal window

Step 1. Open the Terminal.  Add the ssh details along with your IP address to connect the instance through the terminal. Remember to put your actually iPlant username in place of the text 'username' and 'IPaddress' in this next line of code:

$ ssh <username>@<IPaddress>

Step 2. You will find test data in "/opt/quast-4.0/test_data" folder. List its contents with the ls command. 

$ ls /opt/quast-4.0/test_data/
contigs_1.fasta  genes.gff   genes.txt             meta_contigs_2.fasta  meta_ref_2.fasta  operons.gff  reads1.fastq.gz  reference.fasta.gz
contigs_2.fasta  genes.ncbi  meta_contigs_1.fasta  meta_ref_1.fasta      meta_ref_3.fasta  operons.txt  reads2.fastq.gz

We'll change to the test_data directory for the remaining steps.

$ cd /opt/quast-4.0/

Part 3: Run Quast-4.0

1. Basic testing 

$ python quast.py -o ~/quast_test_output -R test_data/reference.fasta.gz -G test_data/genes.gff test_data/contigs_1.fasta test_data/contigs_2.fasta

$ python quast.py -o ~/quast_test_output_sv -R /opt/quast-4.0/test_data/reference.fasta.gz -O /opt/quast-4.0/test_data/operons.gff -G /opt/quast-4.0/test_data/genes.gff --gage  --gene-finding  --eukaryote  --glimmer  -1 /opt/quast-4.0/test_data/reads1.fastq.gz -2 /opt/quast-4.0/test_data/reads2.fastq.gz /opt/quast-4.0/test_data/contigs_1.fasta /opt/quast-4.0/test_data/contigs_2.fasta

$ python metaquast.py -o ~/metaquast_test_output -R /opt/quast-4.0/test_data/meta_ref_1.fasta,/opt/quast-4.0/test_data/meta_ref_2.fasta,/opt/quast-4.0/test_data/meta_ref_3.fasta /opt/quast-4.0/test_data/meta_contigs_1.fasta /opt/quast-4.0/test_data/meta_contigs_2.fasta

$ sudo python metaquast.py -o ~/metaquast_test_output_no_ref /opt/quast-4.0/test_data/meta_contigs_1.fasta /opt/quast-4.0/test_data/meta_contigs_2.fasta