Idba
Introduction
Idba
is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
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.
Versions
1.1.3
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
Module
You can load the modules by:
module load biocontainers
module load idba
Example job
Warning
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