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Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current technique...

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Autores principales: Al-Nakeeb, Kosai, Petersen, Thomas Nordahl, Sicheritz-Pontén, Thomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699183/
https://www.ncbi.nlm.nih.gov/pubmed/29162031
http://dx.doi.org/10.1186/s12859-017-1927-y
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author Al-Nakeeb, Kosai
Petersen, Thomas Nordahl
Sicheritz-Pontén, Thomas
author_facet Al-Nakeeb, Kosai
Petersen, Thomas Nordahl
Sicheritz-Pontén, Thomas
author_sort Al-Nakeeb, Kosai
collection PubMed
description BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS: Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. CONCLUSION: Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1927-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-56991832017-12-01 Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data Al-Nakeeb, Kosai Petersen, Thomas Nordahl Sicheritz-Pontén, Thomas BMC Bioinformatics Software BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS: Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. CONCLUSION: Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1927-y) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-21 /pmc/articles/PMC5699183/ /pubmed/29162031 http://dx.doi.org/10.1186/s12859-017-1927-y Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Al-Nakeeb, Kosai
Petersen, Thomas Nordahl
Sicheritz-Pontén, Thomas
Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title_full Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title_fullStr Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title_full_unstemmed Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title_short Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
title_sort norgal: extraction and de novo assembly of mitochondrial dna from whole-genome sequencing data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699183/
https://www.ncbi.nlm.nih.gov/pubmed/29162031
http://dx.doi.org/10.1186/s12859-017-1927-y
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