idba
Link to section 'Introduction' of 'idba' Introduction
Idba is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinformatics.
For more information, please check its website: https://biocontainers.pro/tools/idba and its home page: https://i.cs.hku.hk/~alse/hkubrg/projects/idba/index.html.
Link to section 'Versions' of 'idba' Versions
- 1.1.3
Link to section 'Commands' of 'idba' Commands
- fa2fq
- filter_blat
- filter_contigs
- filterfa
- fq2fa
- idba
- idba_hybrid
- idba_tran
- idba_tran_test
- idba_ud
- parallel_blat
- parallel_rna_blat
- print_graph
- raw_n50
- run-unittest.py
- sample_reads
- scaffold
- scan.py
- shuffle_reads
- sim_reads
- sim_reads_tran
- sort_psl
- sort_reads
- split_fa
- split_fq
- split_scaffold
- test
- validate_blat
- validate_blat_parallel
- validate_component
- validate_contigs_blat
- validate_contigs_mummer
- validate_reads_blat
- validate_rna
Link to section 'Module' of 'idba' Module
You can load the modules by:
module load biocontainers
module load idba
Link to section 'Example job' of 'idba' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Idba on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=idba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers idba
fq2fa --paired --filter SRR1977249.abundtrim.subset.pe.fq SRR1977249.abundtrim.subset.pe.fa
idba_ud -r SRR1977249.abundtrim.subset.pe.fa -o output