Idba

Introduction

Idba is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/idba
Home page: https://i.cs.hku.hk/~alse/hkubrg/projects/idba/index.html

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.1.3

BELL

1.1.3

GAUTSCHI

1.1.3

NEGISHI

1.1.3

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers idba

# Your idba workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers idba

# Your idba workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers idba

# Your idba workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers idba

# Your idba workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers idba

# Your idba workflow...