Large scale loss of data in low-diversity Illumina sequencing libraries can be recovered by deferred cluster calling
Open accessAbstract
Massively parallel DNA sequencing is capable of sequencing tens of millions of DNA fragments at the same time. However, sequence bias in the initial cycles, which are used to determine the coordinates of individual clusters, causes a loss of fidelity in cluster identification on Illumina Genome Analysers. This can result in a significant reduction in the numbers of clusters that can be analysed. Such low sample diversity is an intrinsic problem of sequencing libraries that are generated by restriction enzyme digestion, such as e4C-seq or reduced-representation libraries. Similarly, this problem can also arise through the combined sequencing of barcoded, multiplexed libraries. We describe a procedure to defer the mapping of cluster coordinates until low-diversity sequences have been passed. This simple procedure can recover substantial amounts of next generation sequencing data that would otherwise be lost.
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High sequence similarity in amplicon sequencing can lead to decreased sequence quality on Illumina platforms.
“High sequence similarity in in amplicon sequencing can lead to decreased sequence quality on Illumina platforms [40].”
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Elbrecht, V., & Leese, F. (2015) · PLOS ONE · doi:10.1371/journal.pone.0130324 · Cited by 765 · see citing works
- Authors
- Krueger, F., Andrews, S. R., & Osborne, C. S.
- Affiliations
- Babraham Institute (GB)
- Corresponding author
- Osborne, Cameron S.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-01-28
- Volume
- 6
- Issue
- 1
- Pages
- e16607
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3030592
- OpenAlex
- W2027589602
- Cited by
- 102
- References
- 7
- Citations by year
- 2025: 3 · 2024: 4 · 2023: 10 · 2022: 4 · 2021: 4 · 2020: 14 · 2019: 7 · 2018: 6 · 2017: 8 · 2016: 11 · 2015: 11 · 2014: 9 · 2013: 3 · 2012: 6
- FWCI
- 2.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Portal (King's College London) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Leukaemia and Lymphoma Research
- Biotechnology and Biological Sciences Research Council (BBS/E/B/0000H212)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- sequence bias, cluster detection, reduced representation sequencing, data recovery, restriction enzyme digestion
- MeSH terms
- Data Collection, Restriction Mapping, Gene Library, Cluster Analysis, Sequence Analysis, DNA, DNA Barcoding, Taxonomic
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