IDBA-UD
作者： Y. Peng , H. C. M. Leung , S. M. Yiu , F. Y. L. Chin
DOI: 10.1093/BIOINFORMATICS/BTS174
关键词:
摘要: Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell or metagenomic technologies. However, both technologies suffer the problem that depth of different regions genome genomes species are highly uneven. Most existing assemblers usually have an assumption depths even. These fail construct correct long contigs. Results: We introduce IDBA-UD algorithm is based on de Bruijn graph approach for assembling with uneven depths. Several non-trivial techniques been employed tackle problems. Instead simple threshold, we use multiple depthrelative thresholds remove erroneous k-mers in low-depth and high-depth regions. The technique local assembly paired-end information used solve branch short repeat To speed up process, error correction step conducted can be aligned highconfident contigs. Comparison performances (Velvet, Velvet-SC, SOAPdenovo Meta-IDBA) datasets, shows reconstruct longer contigs higher accuracy. Availability: toolkit available at our website http://www.cs.hku.hk/~alse/idba_ud Contact: chin@cs.hku.hk
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acm.org 参考文章(21)
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