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. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.

The basic IDBA is included only for comparison.

• If you are assembling genomic data without reference, please use IDBA-UD.
• If you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.
• If you are assembling transcriptome data, please use IDBA-Tran.

References:

• Peng, Y., et al. (2010) IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. RECOMB. Lisbon. doi: 10.1007/978-3-642-12683-3_28
• Peng, Y., et al. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420-1428.Paper, doi: 10.1093/bioinformatics/bts174

• IDBA suite on GitHub
• IDBA
• IDBA-UD
• IDBA-Hybrid
• IDBA-Tran

• Module Name: idba (see the modules page for more information)
  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  Allocate an interactive session and run the program.
  Sample session (user input in bold):

  [user@biowulf]$ sinteractive
  salloc.exe: Pending job allocation 46116226
  salloc.exe: job 46116226 queued and waiting for resources
  salloc.exe: job 46116226 has been allocated resources
  salloc.exe: Granted job allocation 46116226
  salloc.exe: Waiting for resource configuration
  salloc.exe: Nodes cn3144 are ready for job
  [user@cn3144 ~]$ module load idba
  [user@cn3144 ~]$ idba_ud  -r reads.fa -o output
  [user@cn3144 ~]$ exit
  salloc.exe: Relinquishing job allocation 46116226
  [user@biowulf ~]$
  

  Batch job
  Most jobs should be run as batch jobs.

  Create a batch input file (e.g. TEMPLATE.sh). For example:

  #!/bin/bash
  set -e
  module load idba
  idba_ud  -r read.fa -o output
  

  Submit this job using the Slurm sbatch command.

  sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh

  Swarm of Jobs
  A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

  Create a swarmfile (e.g. idba.swarm). For example:

  idba_ud  -r sample1-reads.fa -o sample1
  idba_ud  -r sample2-reads.fa -o sample2
  idba_ud  -r sample3-reads.fa -o sample3
  idba_ud  -r sample4-reads.fa -o sample4
  

  Submit this job using the swarm command.

  swarm -f idba.swarm [-g #] [-t #] --module idba

  where

  -g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
  -t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
  --module idba	Loads the IDBA module for each subjob in the swarm