{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T23:04:39Z","timestamp":1776467079887,"version":"3.51.2"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.<\/jats:p>\n               <jats:p>Results: We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy.<\/jats:p>\n               <jats:p>Availability: The IDBA-UD toolkit is available at our website http:\/\/www.cs.hku.hk\/~alse\/idba_ud<\/jats:p>\n               <jats:p>Contact: \u00a0chin@cs.hku.hk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts174","type":"journal-article","created":{"date-parts":[[2012,4,12]],"date-time":"2012-04-12T05:16:27Z","timestamp":1334207787000},"page":"1420-1428","source":"Crossref","is-referenced-by-count":2807,"title":["IDBA-UD: a <i>de novo<\/i> assembler for single-cell and metagenomic sequencing data with highly uneven depth"],"prefix":"10.1093","volume":"28","author":[{"given":"Yu","family":"Peng","sequence":"first","affiliation":[{"name":"Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong"}]},{"given":"Henry C. M.","family":"Leung","sequence":"additional","affiliation":[{"name":"Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong"}]},{"given":"S. M.","family":"Yiu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong"}]},{"given":"Francis Y. 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