SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments

OBJECTIVE: The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algor...

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Autores principales: Angelova, Nelina, Danis, Theodoros, Lagnel, Jacques, Tsigenopoulos, Costas S., Manousaki, Tereza
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Research Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900408/
https://www.ncbi.nlm.nih.gov/pubmed/35255960
http://dx.doi.org/10.1186/s13104-022-05978-5
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author Angelova, Nelina
Danis, Theodoros
Lagnel, Jacques
Tsigenopoulos, Costas S.
Manousaki, Tereza
author_facet Angelova, Nelina
Danis, Theodoros
Lagnel, Jacques
Tsigenopoulos, Costas S.
Manousaki, Tereza
author_sort Angelova, Nelina
collection PubMed
description OBJECTIVE: The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. RESULTS: Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-022-05978-5.
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spelling pubmed-89004082022-03-17 SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments Angelova, Nelina Danis, Theodoros Lagnel, Jacques Tsigenopoulos, Costas S. Manousaki, Tereza BMC Res Notes Research Note OBJECTIVE: The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. RESULTS: Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-022-05978-5. BioMed Central 2022-03-07 /pmc/articles/PMC8900408/ /pubmed/35255960 http://dx.doi.org/10.1186/s13104-022-05978-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Note
Angelova, Nelina
Danis, Theodoros
Lagnel, Jacques
Tsigenopoulos, Costas S.
Manousaki, Tereza
SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title_full SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title_fullStr SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title_full_unstemmed SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title_short SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
title_sort snakecube: containerized and automated pipeline for de novo genome assembly in hpc environments
topic Research Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900408/
https://www.ncbi.nlm.nih.gov/pubmed/35255960
http://dx.doi.org/10.1186/s13104-022-05978-5
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