IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
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Summary
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.
- Type
- article
- Published
- 2012-06-01
- Cited by
- 2,828
- References
- 21
- Access
- Open access
- OpenAlex
- https://openalex.org/W2141920662
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1591391
Keywords
Contig, Metagenomics, De Bruijn graph, Sequence assembly, Hybrid genome assembly
References
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- Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
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- Quake: quality-aware detection and correction of sequencing errors
- Assemblathon 1: a competitive assessment of de novo short read assembly methods.
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- An Eulerian path approach to DNA fragment assembly
- Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
- Short read fragment assembly of bacterial genomes.
- Error correction of high-throughput sequencing datasets with non-uniform coverage
- Phenotypic connections in surprising places
- Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
- De novo assembly of human genomes with massively parallel short read sequencing.
- MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes
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- Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis
- Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
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- Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil.
- MR-CUDASW - GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data
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