{"id":4601,"date":"2018-03-19T11:27:27","date_gmt":"2018-03-19T11:27:27","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4601"},"modified":"2018-03-19T11:58:59","modified_gmt":"2018-03-19T11:58:59","slug":"idba","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/idba\/","title":{"rendered":"IDBA and IDBA-UD"},"content":{"rendered":"

Overview<\/h2>\n

IDBA<\/a> is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions.<\/p>\n

Version 1.2.0 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all usage should adhere to that license.<\/p>\n

Set up procedure<\/h2>\n

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

\r\nmodule load apps\/intel-15.0\/idba\/1.2.0\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run IDBA on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
The following executables are available. To see a list of flags accepted by each executable you may run them on the login node with the --help<\/code> flag:<\/p>\n
\r\nfa2fq           idba_hybrid        print_graph    sim_reads_tran  validate_component\r\nfilter_blat     idba_tran          raw_n50        sort_psl        validate_contigs_blat\r\nfilter_contigs  idba_tran_test     sample_reads   sort_reads      validate_contigs_mummer\r\nfilterfa        idba_ud            scaffold       split_fa        validate_reads_blat\r\nfq2fa           parallel_blat      shuffle_reads  split_fq        validate_rna\r\nidba            parallel_rna_blat  sim_reads      split_scaffold\r\n<\/pre>\n
A number of helper scripts are available – run the following command after loading the modulefile to see what they are:<\/p>\n
\r\nls $IDBADIR\/script\/\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -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 the number of cores requested (1 in a serial job)\r\nidba_ud --num_threads $NSLOTS -r read.fa<\/em> -o output_dir<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -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 (can be 2--24)\r\n\r\n# $NSLOTS will be set to the number of cores requested (1 in a serial job)\r\nidba_ud --num_threads $NSLOTS -r read.fa<\/em> -o output_dir<\/em>\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