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Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data
BACKGROUND: Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451199/ https://www.ncbi.nlm.nih.gov/pubmed/30821816 http://dx.doi.org/10.1093/gigascience/giz014 |
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author | Korhonen, Pasi K Hall, Ross S Young, Neil D Gasser, Robin B |
author_facet | Korhonen, Pasi K Hall, Ross S Young, Neil D Gasser, Robin B |
author_sort | Korhonen, Pasi K |
collection | PubMed |
description | BACKGROUND: Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. FINDINGS: We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. CONCLUSIONS: This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes. |
format | Online Article Text |
id | pubmed-6451199 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-64511992019-04-09 Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data Korhonen, Pasi K Hall, Ross S Young, Neil D Gasser, Robin B Gigascience Technical Note BACKGROUND: Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. FINDINGS: We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. CONCLUSIONS: This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes. Oxford University Press 2019-03-01 /pmc/articles/PMC6451199/ /pubmed/30821816 http://dx.doi.org/10.1093/gigascience/giz014 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Technical Note Korhonen, Pasi K Hall, Ross S Young, Neil D Gasser, Robin B Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title | Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title_full | Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title_fullStr | Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title_full_unstemmed | Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title_short | Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data |
title_sort | common workflow language (cwl)-based software pipeline for de novo genome assembly from long- and short-read data |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451199/ https://www.ncbi.nlm.nih.gov/pubmed/30821816 http://dx.doi.org/10.1093/gigascience/giz014 |
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