Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results
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Summary
This extensive analysis demonstrates that, in addition to sequencing coverage, attributes such as the architecture of the target genome, the identity of the used assembly program, the average read length and the observed sequencing error rates are powerful variables that affect the best achievable assembly of thetarget sequence in terms of size and correctness.
- Type
- article
- Published
- 2011-09-07
- Cited by
- 42
- References
- 29
- Access
- Open access
- OpenAlex
- https://openalex.org/W21915294
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1632534
Keywords
Medicine
References
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- Partial Sequence Analysis of 130 Randomly Selected Maize cDNA Clones
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- DNA sequencing with chain-terminating inhibitors.
- SOAP: short oligonucleotide alignment program
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Cited by
- Fuzzy k-mers and their application to comparative genome assembly
- BAC sequencing using pooled methods.
- An Integrated Approach to Comparative Assembly
- Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
- Parallel Machine Learning Algorithms In Bioinformatics And Global Optimization
- Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine
- Impact of analytic provenance in genome analysis
- GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
- Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data
- ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
- TIGER: tiled iterative genome assembler
- Sequence assembly demystified
- Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference
- Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing
- Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
- Automatic Outlier Detection for Genome Assembly Quality Assessment
- Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
- in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies
- On the origin of hops : genetic variability, phylogenetic relationships, and ecological plasticity of Humulus (Cannabaceae)
- Next Generation Sequencing Technologies and Challenges in Sequence Assembly
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