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