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Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes

Multi-CSAR is a web server that can efficiently and more accurately order and orient the contigs in the assembly of a target genome into larger scaffolds based on multiple reference genomes. Given a target genome and multiple reference genomes, Multi-CSAR first identifies sequence markers shared bet...

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Detalles Bibliográficos
Autores principales: Liu, Shu-Cheng, Ju, Yan-Ru, Lu, Chin Lung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252826/
https://www.ncbi.nlm.nih.gov/pubmed/35524553
http://dx.doi.org/10.1093/nar/gkac301
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author Liu, Shu-Cheng
Ju, Yan-Ru
Lu, Chin Lung
author_facet Liu, Shu-Cheng
Ju, Yan-Ru
Lu, Chin Lung
author_sort Liu, Shu-Cheng
collection PubMed
description Multi-CSAR is a web server that can efficiently and more accurately order and orient the contigs in the assembly of a target genome into larger scaffolds based on multiple reference genomes. Given a target genome and multiple reference genomes, Multi-CSAR first identifies sequence markers shared between the target genome and each reference genome, then utilizes these sequence markers to compute a scaffold for the target genome based on each single reference genome, and finally combines all the single reference-derived scaffolds into a multiple reference-derived scaffold. To run Multi-CSAR, the users need to upload a target genome to be scaffolded and one or more reference genomes in multi-FASTA format. The users can also choose to use the ‘weighting scheme of reference genomes’ for Multi-CSAR to automatically calculate different weights for the reference genomes and choose either ‘NUCmer on nucleotides’ or ‘PROmer on translated amino acids’ for Multi-CSAR to identify sequence markers. In the output page, Multi-CSAR displays its multiple reference-derived scaffold in two graphical representations (i.e. Circos plot and dotplot) for the users to visually validate the correctness of scaffolded contigs and in a tabular representation to further validate the scaffold in detail. Multi-CSAR is available online at http://genome.cs.nthu.edu.tw/Multi-CSAR/.
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spelling pubmed-92528262022-07-05 Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes Liu, Shu-Cheng Ju, Yan-Ru Lu, Chin Lung Nucleic Acids Res Web Server Issue Multi-CSAR is a web server that can efficiently and more accurately order and orient the contigs in the assembly of a target genome into larger scaffolds based on multiple reference genomes. Given a target genome and multiple reference genomes, Multi-CSAR first identifies sequence markers shared between the target genome and each reference genome, then utilizes these sequence markers to compute a scaffold for the target genome based on each single reference genome, and finally combines all the single reference-derived scaffolds into a multiple reference-derived scaffold. To run Multi-CSAR, the users need to upload a target genome to be scaffolded and one or more reference genomes in multi-FASTA format. The users can also choose to use the ‘weighting scheme of reference genomes’ for Multi-CSAR to automatically calculate different weights for the reference genomes and choose either ‘NUCmer on nucleotides’ or ‘PROmer on translated amino acids’ for Multi-CSAR to identify sequence markers. In the output page, Multi-CSAR displays its multiple reference-derived scaffold in two graphical representations (i.e. Circos plot and dotplot) for the users to visually validate the correctness of scaffolded contigs and in a tabular representation to further validate the scaffold in detail. Multi-CSAR is available online at http://genome.cs.nthu.edu.tw/Multi-CSAR/. Oxford University Press 2022-05-07 /pmc/articles/PMC9252826/ /pubmed/35524553 http://dx.doi.org/10.1093/nar/gkac301 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Liu, Shu-Cheng
Ju, Yan-Ru
Lu, Chin Lung
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title_full Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title_fullStr Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title_full_unstemmed Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title_short Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
title_sort multi-csar: a web server for scaffolding contigs using multiple reference genomes
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252826/
https://www.ncbi.nlm.nih.gov/pubmed/35524553
http://dx.doi.org/10.1093/nar/gkac301
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