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.
Keywords for this software
References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
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- Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.: Bidirectional variable-order de Bruijn graphs (2018)
- Bonizzoni, Paola; Della Vedova, Gianluca; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella: An external-memory algorithm for string graph construction (2017)
- Jean, Géraldine; Radulescu, Andreea; Rusu, Irena: The contig assembly problem and its algorithmic solutions (2017)
- Nimmy, Sonia Farhana; Kamal, M. S.: Next generation sequencing under de novo genome assembly (2015)