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Grant support

We would like to thank N. Alvarez and A. Mastretta-Yanes for fruitful discussions and support. This work was supported in part by Spanish MINECO grant CGL2013-42589-P cofinanced by FEDER, and FPI studentship BES-2014-067868.

Analysis of institutional authors

Lopez De Heredia, U.Author

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June 9, 2019
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DDRADSEQTOOLS: a software package for in silico simulation and testing of double-digest RADseq experiments

Publicated to:Molecular Ecology Resources. 17 (2): 230-246 - 2017-03-01 17(2), DOI: 10.1111/1755-0998.12550

Authors: Mora-Marquez, F; Garcia-Olivares, V; Emerson, B C; Lopez de Heredia, U

Affiliations

IPNA CSIC, Isl Ecol & Evolut Res Grp, Tenerife, Canary Islands, Spain - Author
Tech Univ Madrid UPM, Forest Genet & Physiol Res Grp, Ciudad Univ S-N, Madrid, Spain - Author
Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England - Author

Abstract

Double-digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present DDRADSEQTOOLS, a software package to help ddRADseq experimental design by (i) the generation of in silico double-digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. DDRADSEQTOOLS generates single-end (SE) or paired-end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine-tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. DDRADSEQTOOLS is cost-efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.

Keywords

allele dropoutcoveragedouble-digested radseqpcr duplicatesAllele dropoutComputational biologyCoverageDnaDna restriction enzymesDouble-digested radseqFormatGeneticsHigh-throughput nucleotide sequencingIn silico simulationLociMarkersPcr duplicatesPopulation genomicsSequenceSnp discoverySoftware

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Ecology Resources due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2017, it was in position 8/160, thus managing to position itself as a Q1 (Primer Cuartil), in the category Ecology. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations from Scopus Elsevier, it yields a value for the Field-Weighted Citation Impact from the Scopus agency: 1.2, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Field Citation Ratio (FCR) from Dimensions: 3.55 (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-17, the following number of citations:

  • WoS: 25
  • Scopus: 26
  • Europe PMC: 11
  • Google Scholar: 48

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-17:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 157.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 157 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 13.35.
  • The number of mentions on the social network X (formerly Twitter): 10 (Altmetric).

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Mora-Marquez, F.) and Last Author (LOPEZ DE HEREDIA LARREA, UNAI).