{"id":4643,"date":"2018-04-10T09:54:16","date_gmt":"2018-04-10T09:54:16","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4643"},"modified":"2018-04-10T10:11:00","modified_gmt":"2018-04-10T10:11:00","slug":"quast","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/quast\/","title":{"rendered":"Quast and MetaQuast"},"content":{"rendered":"

Quast<\/a> is a program to evaluate genome assemblies. QUAST works both with and without a reference genome. The tool accepts multiple assemblies, thus is suitable for comparison. This installation also includes MetaQuast, which evaluates and compares metagenome assemblies based on alignments to close references, and Icarus, a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies.<\/p>\n

Version 4.6.3 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

Version 4.6.3 of QUAST was released under GPL v2 on 6 February 2018. Note that some of build-in third-party tools are not under GPL v2. See LICENSE<\/a> for details.<\/p>\n

Please cite your usage of the various tools using the citation information on the Quast website<\/a>.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\nmodule load apps\/gcc\/python-packages\/anaconda3-5.1.0\/quast\/4.6.3\r\n<\/pre>\n
This will automatically load the Anaconda python modulefile for you, which provides python 3.6.4.<\/p>\n
Running the application<\/h2>\n
Please do not run Quast or MetaQuast on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# $NSLOTS will be set to 1 in a serial job.\r\n# You MUST inform quast how many cores it can use.\r\nquast.py -t $NSLOTS contigs_1.fasta contigs_2.fasta<\/em>  -R reference.fasta.gz<\/em> -G genes.gff<\/em>\r\n  #\r\n  # Use metaquast.py to run MetaQuast\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores (2-24)\r\n\r\n# $NSLOTS will be set to the number given on the -pe line above.\r\n# You MUST inform quast how many cores it can use.\r\nquast.py -t $NSLOTS contigs_1.fasta contigs_2.fasta<\/em>  -R reference.fasta.gz<\/em> -G genes.gff<\/em>\r\n  #\r\n  # Use metaquast.py to run MetaQuast\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n