IDBA-UD¶

Description¶

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.

Environment Modules¶

Run module spider idba-ud to find out what environment modules are available for this application.

Environment Variables¶

HPC_IDBA_UD_DIR - installation directory
HPC_IDBA_UD_BIN - executable directory

Categories¶

genomics, phylogenetics