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Analysis of institutional authors

Mora-Marquez, FAuthorDe Heredia, UlCorresponding Author

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May 24, 2021
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NGScloud2: optimized bioinformatic analysis using Amazon Web Services

Publicated to: Peerj. 9 e11237- - 2021-04-16 9(), DOI: 10.7717/peerj.11237

Authors:

Mora-Marquez, Fernando; Luis Vazquez-Poletti, Jose; Lopez de Heredia, Unai
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Affiliations

Univ Complutense Madrid, Fac Informat, Dept Arquitectura Ordenadores & Automat, GI Arquitectura Sistemas Distribuidos, Madrid, Spain - Author
Univ Politecn Madrid, Dept Sistemas & Recursos Nat, GI Sistemas Nat & Hist Forestal, ETSI Montes Forestal & Medio Nat, Madrid, Spain - Author

Abstract

Background. NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods. NGScloud2 presents major technical improvements, such as the possibility of running spot instances and the most updated AWS instances types, that can lead to significant cost savings. As compared to its initial implementation, this improved version updates and includes common applications for de novo RNAseq analysis, and incorporates tools to operate workflows of bioinformatic analysis of referencebased RNAseq, RADseq and functional annotation. NGScloud2 optimizes the access to Amazon's large computing infrastructures to easily run popular bioinformatic software applications, otherwise inaccessible to non-specialized users lacking suitable hardware infrastructures. Results. The correct performance of the pipelines for de novo RNAseq, referencebased RNAseq, RADseq and functional annotation was tested with real experimental data, providing workflow performance estimates and tips to make optimal use of NGScloud2. Further, we provide a qualitative comparison of NGScloud2 vs. the Galaxy framework. NGScloud2 code, instructions for software installation and use are available at https://github.com/GGFHF/NGScloud2. NGScloud2 includes a companion package, NGShelper that contains Python utilities to post-process the output of the pipelines for downstream analysis at https://github.com/GGFHF/NGShelper.
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Keywords

AlignmentArticleAwsBig dataBioinformaticsCloud computingCost controlExpression analysisFunctional annotationGeneHigh throughput sequencingNext generation sequencingPackagePipelineProteinQuality assessment-toolRna sequencingRna-seq dataRunningSequenceSoftwareTranscriptomicsWorkflow

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Peerj due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Agricultural and Biological Sciences (Miscellaneous).

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-12-21:

  • Google Scholar: 5
  • WoS: 6
  • Scopus: 5
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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 2025-12-21:

  • 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: 19.
  • 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: 19 (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: 5.
  • The number of mentions on the social network X (formerly Twitter): 7 (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.
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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 (MORA MARQUEZ, FERNANDO) and Last Author (LOPEZ DE HEREDIA LARREA, UNAI).

the author responsible for correspondence tasks has been LOPEZ DE HEREDIA LARREA, UNAI.

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Awards linked to the item

This work was supported by the Spanish Ministry of Economy and Competitiveness-MINECO [grant number AGL2015-67495-C2-2-R]; the Spanish Ministry of Science and Innovation [grant numbers PID2019-110330GB-C22 and RTI2018-096465-B-I00]; the Regional Government of Madrid [grant numbers P2018/TCS4499 and S2018/TCS-4499]; and by an Amazon Research Grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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