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Contract Grant Sponsors: Spanish Ministry of Economy and Competitiveness; Generalitat de Catalunya; European Regional Development Fund (ERDF); RD-Connect Project (EC FP7/2007-2013 #305444); ELIXIR-EXCELERATE (EC H2020 #676559); MICINN (TIN2014-53234- C2-1-R).

Analysis of institutional authors

Laurie, SAuthorMarco-Sola SAuthorBeltrán SCorresponding AuthorTrotta, JrAuthorCamps JAuthorGut M.AuthorHeath SAuthorGut I.Corresponding Author

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March 25, 2020
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Article

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Publicated to:Human Mutation. 37 (12): 1263-1271 - 2016-12-01 37(12), DOI: 10.1002/humu.23114

Authors: Laurie, S; Fernandez-Callejo, M; Marco-Sola, S; Trotta, JR; Camps, J; Chacón, A; Espinosa, A; Gut, M; Gut, I; Heath, S; Beltran, S

Affiliations

BIST, Ctr Genom Regulat CRG, CNAG CRG, Baldiri & Reixac 4, Barcelona 08028, Spain - Author
Univ Autonoma Barcelona, Bellaterra, Spain - Author
UPF, Barcelona, Spain - Author
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Abstract

As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample. Results have been compared between them and against the NIST Genome in a Bottle (GIAB) variants reference dataset. We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome. SNV, and especially InDel, detection is less reliable in 20% of the genome, and almost unfeasible in the remaining 10%. These findings will aid in choosing the appropriate tools bearing in mind objectives, workload, and computing infrastructure available.© 2016 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Keywords

AlignmentBenchmarkBioinformaticsComputational biologyComputing speedDiscoveryExomeFrameworkGenerationGenetic variationGenome, humanHigh-throughput nucleotide sequencingHumansNa12878NgsSequence analysis, dnaSnpSoftwareVariant callingWhole exome sequencingWhole genome sequencing

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Human Mutation 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, 2016, it was in position 29/167, thus managing to position itself as a Q1 (Primer Cuartil), in the category Genetics & Heredity.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 1.32. This 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:

  • Weighted Average of Normalized Impact by the Scopus agency: 1.24 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 5.4 (source consulted: Dimensions Oct 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-10-13, the following number of citations:

  • WoS: 44
  • Scopus: 44
  • Europe PMC: 25

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 2025-10-13:

  • 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: 152.
  • 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: 152 (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: 22.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 12 (Altmetric).
  • The number of mentions in news outlets: 2 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

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 (LAURIE, STEVEN) and Last Author (Gut, Ivo).

the authors responsible for correspondence tasks have been Beltran AGULLÓ, Sergi and Gut, Ivo.