IDBA-UD 1.1.3-GCCcore-12.3.0

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

Accessing IDBA-UD 1.1.3-GCCcore-12.3.0

To load the module for IDBA-UD 1.1.3-GCCcore-12.3.0 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2023a
module load IDBA-UD/1.1.3-GCCcore-12.3.0

BEAR Apps Version

2023a

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two parts: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

More Information

For more information visit the IDBA-UD website.

Dependencies

This version of IDBA-UD has a direct dependency on: GCCcore/12.3.0

Required By

This version of IDBA-UD is a direct dependent of: MaxBin/2.2.7-gompi-2023a-Python-2.7.18

Last modified on 4th March 2025