IDBA-UD

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.

homepage: https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

version	toolchain
1.1.3	GCC/10.2.0
1.1.3	GCC/10.3.0
1.1.3	GCC/11.2.0
1.1.3	GCC/8.2.0-2.31.1
1.1.3	GCC/8.3.0
1.1.3	GCC/9.3.0
1.1.3	foss/2018a
1.1.3	foss/2018b

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