De novo fragment assembly with short mate-paired reads: Does the read length matter?
Open accessAbstract
Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length ≈ GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We describe a new tool, EULER-USR, for assembling mate-paired short reads and use it to analyze the question of whether the read length matters. We further complement the ongoing experimental efforts to maximize read length by a new computational approach for increasing the effective read length. While the common practice is to trim the error-prone tails of the reads, we present an approach that substitutes trimming with error correction using repeat graphs. An important and counterintuitive implication of this result is that one may extend sequencing reactions that degrade with length “past their prime” to where the error rate grows above what is normally acceptable for fragment assembly.
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High-throughput sequencing strategies can be adapted to generate transcriptome data, either by aligning cDNA to an assembled genome or through de novo assembly.
“high-throughput sequencing strategies can be adapted to generate transcriptome data, either by aligning cDNA sequence data to an assembled genome or through de novo transcriptome assembly [111,112]”
From Biofuels from algae: Challenges and potential (2010) · cites this paper as [111]
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- Authors
- Chaisson, M. J., Brinza, D., & Pevzner, P. A.
- Affiliations
- University of California San Diego (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-12-03
- Volume
- 19
- Issue
- 2
- Pages
- 336-346
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2652199
- OpenAlex
- W2097529842
- Cited by
- 279
- References
- 33
- Citations by year
- 2025: 4 · 2024: 2 · 2023: 3 · 2022: 6 · 2021: 4 · 2020: 2 · 2019: 9 · 2018: 10 · 2017: 12 · 2016: 21 · 2015: 19 · 2014: 27 · 2013: 28 · 2012: 38
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0303622)
- National Institutes of Health
- National Human Genome Research Institute (R21HG004130)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- de novo genome assembly, error correction, read trimming, sequencing error rate
- MeSH terms
- Algorithms, Base Sequence, Chromosome Mapping, Escherichia coli, Genetic Markers, Models, Biological, Bias, Sequence Alignment, Genome, Bacterial, Sequence Analysis, DNA, Computational Biology, Base Pairing
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