The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Addressing challenges in the production and analysis of illumina sequencing data
Open accessAbstract
Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq) represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with.
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Cites
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Cited by
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443
The promise and challenge of high-throughput sequencing of the antibody repertoire
Georgiou, G., Ippolito, G. C., Beausang, J., Busse, C. E., Wardemann, H., & Quake, S. R. (2014) · Nature Biotechnology · doi:10.1038/nbt.2782 · Cited by 652
Early life dynamics of the human gut virome and bacterial microbiome in infants
Lim, E. S., Zhou, Y., Zhao, G., Bauer, I. K., Droit, L., Ndao, I. M., Warner, B. B., Tarr, P. I., Wang, D., & Holtz, L. R. (2015) · Nature Medicine · doi:10.1038/nm.3950 · Cited by 658
DNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608
Self-citationSingle-stranded DNA library preparation for the sequencing of ancient or damaged DNA
Gansauge, M.-T., & Meyer, M. (2013) · Nature Protocols · doi:10.1038/nprot.2013.038 · Cited by 561
Metadata
- Authors
- Kircher, M., Heyn, P., & Kelso, J.
- Venue
- BMC Genomics
- Published
- 2011-07-29
- Volume
- 12
- Issue
- 1
- Pages
- 382-382
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2095267560
- Cited by
- 162
- References
- 7
- FWCI
- 4.82
- Type
- journal article
- Language
- en
- Open access
- gold
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