Information de reference pour ce titreAccession Number: | 00124336-201228110-00002.
|
Author: | Peng, Yu; Leung, Henry C. M.; Yiu, S. M.; Chin, Francis Y. L.
|
Institution: | Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong
|
Title: | IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.[Article]
|
Source: | Bioinformatics. 28(11):1420-1428, June 1, 2012.
|
Abstract: | 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.
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.
Availability: The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_...- ouverture dans une nouvelle fenêtre
Contact: [email protected]
(C) Copyright Oxford University Press 2012.
|
References: | Butler J., et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads Genome Res.. 2008;18:810-820
Chaisson M.J., Pevzner P.A.. Short read fragment assembly of bacterial genomes Genome Res.. 2008;18:324-330
Chaisson M.J., et al. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res.. 2009;19:336-346
Chitsaz H., et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets Nat. Biotechnol.. 2011;29:915-921
Earl D., et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods Genome Res.. 2011;21:2224-2241
Hernandez D., et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer Genome Res.. 2008;18:802-809
Kelley D.R., et al. Quake: quality-aware detection and correction of sequencing errors Genome Biol.. 2010;11:R116
Kent W.J.. BLAT-the BLAST-like alignment tool Genome Res.. 2002;12:656-664
Li R., et al. De novo assembly of human genomes with massively parallel short read sequencing Genome Res.. 2010;20:265-272
Medvedev P., et al. Error correction of high-throughput sequencing datasets with non-uniform coverage Bioinformatics. 2011;27:i137-i141
Noguchi H., et al. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes DNA Res.. 2008;15:387-396
Peng Y., et al. IDBA - a practical iterative de Bruijn graph de novo assembler RECOMB. 2010 Lisbon
Peng Y., et al. Meta-IDBA: a de Novo assembler for metagenomic data Bioinformatics. 2011;27:i94-i101
Pevzner P.A., et al. An Eulerian path approach to DNA fragment assembly Proc. Natl Acad. Sci. USA. 2001;98:9748-9753
Rodrigue S., et al. Whole genome amplification and de novo assembly of single bacterial cells PLoS One. 2009;4:e6864
Simpson J.T., et al. ABySS: a parallel assembler for short read sequence data Genome Res.. 2009;19:1117-1123
Wooley J.C., et al. A primer on metagenomics PLoS Comput. Biol.. 2010;6:e1000667
Woyke T., et al. Assembling the marine metagenome, one cell at a time PLoS One. 2009;4:e5299
Zerbino D.R., Birney E.. Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res.. 2008;18:821-829
Zerbino D.R., et al. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler PLoS One. 2009;4:e8407
|
Language: | English.
|
Document Type: | HITSEQ PAPERS.
|
Journal Subset: | Life & Biomedical Sciences. Medical Humanities. Science.
|
ISSN: | 1367-4803
|
NLM Journal Code: | cw9, 9808944
|
DOI Number: | https://dx.doi.org/10.1093/bioin...- ouverture dans une nouvelle fenêtre
|
Annotation(s) | |