Logo do repositório
 
Publicação

Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets

2020-12Artigo científico Acesso aberto
Ver registo simples
dc.contributor.authorDe‐Kayne, Rishi
dc.contributor.authorFrei, David
dc.contributor.authorGreenway, Ryan
dc.contributor.authorMendes, Sofia L.
dc.contributor.authorRetel, Cas
dc.contributor.authorFeulner, Philine G. D.
dc.date.accessioned2021-01-20T10:12:21Z
dc.date.available2021-12-01T01:30:34Z
dc.date.issued2020-12
dc.description.abstractTechnological advances in DNA sequencing over the last decade now permit the production and curation of large genomic data sets in an increasing number of nonmodel species. Additionally, these new data provide the opportunity for combining data sets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher throughput of data at a lower per-base cost, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four-channel system to a two-channel system. We caution that when data are combined from these two systems, erroneous guanine base calls that result from the two-channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artefacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever-changing sequencing platform technology.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationDe-Kayne R, Frei D, Greenway R, Mendes SL, Retel C, Feulner PG. Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets. Mol Ecol Resour. 2020;00:1–8. ht t p s://doi.pt_PT
dc.identifier.doi10.1111/1755-0998.13309pt_PT
dc.identifier.urihttp://hdl.handle.net/10451/45862
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.relationSNSF grant 31003A_163446pt_PT
dc.relationEuropean Regional Development Fund and Swiss Confederation grant “SeeWandel: Life in Lake Constance – the past, present and future” within the framework of the Interreg V programme “Alpenrhein Bodensee-Hochrheinpt_PT
dc.relationSwiss Federal Office for the Environment and Eawag Discretionary Funds 1 2018-2022pt_PT
dc.relationFCT grant SFRH/BD/145153/2019pt_PT
dc.titleSequencing platform shifts provide opportunities but pose challenges for combining genomic data setspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.titleMolecular Ecology Resourcespt_PT
rcaap.embargofctO tipo de licença (Standard Licence) envolvido com a editora Wiley para esta revista, não envolvendo pagamento (APC), apenas permite acesso em repositório público do formato 'aceite' (i.e não editado e paginado pela editora) após período de embargo de 12 meses após a data da sua publicação final.pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

Ficheiros

Principais
A mostrar 1 - 1 de 1
Miniatura
Nome:
DeKayneFrei_accepted.pdf
Tamanho:
369.05 KB
Formato:
Adobe Portable Document Format
Ver/Abrir

Coleções

cE3c - Artigos em Revistas Internacionais