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IDBA and IDBA-UD
Overview
IDBA 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.
Version 1.2.0 is installed on the CSF.
Restrictions on use
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.
Set up procedure
To access the software you must first load the modulefile:
module load apps/intel-15.0/idba/1.2.0
Running the application
Please do not run IDBA on the login node. Jobs should be submitted to the compute nodes via batch.
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 flag:
fa2fq idba_hybrid print_graph sim_reads_tran validate_component filter_blat idba_tran raw_n50 sort_psl validate_contigs_blat filter_contigs idba_tran_test sample_reads sort_reads validate_contigs_mummer filterfa idba_ud scaffold split_fa validate_reads_blat fq2fa parallel_blat shuffle_reads split_fq validate_rna idba parallel_rna_blat sim_reads split_scaffold
A number of helper scripts are available – run the following command after loading the modulefile to see what they are:
ls $IDBADIR/script/
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # $NSLOTS will be set to the number of cores requested (1 in a serial job) idba_ud --num_threads $NSLOTS -r read.fa -o output_dir
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores (can be 2--24) # $NSLOTS will be set to the number of cores requested (1 in a serial job) idba_ud --num_threads $NSLOTS -r read.fa -o output_dir
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.