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Plastaumatic: Automating plastome assembly and annotation

Plastome sequence data is most often extracted from plant whole genome sequencing data and need to be assembled and annotated separately from the nuclear genome sequence. In projects comprising multiple genomes, it is labour intense to individually process the plastomes as it requires many steps and...

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Autores principales: Chen, Wenyi, Achakkagari, Sai Reddy, Strömvik, Martina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9669643/
https://www.ncbi.nlm.nih.gov/pubmed/36407635
http://dx.doi.org/10.3389/fpls.2022.1011948
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author Chen, Wenyi
Achakkagari, Sai Reddy
Strömvik, Martina
author_facet Chen, Wenyi
Achakkagari, Sai Reddy
Strömvik, Martina
author_sort Chen, Wenyi
collection PubMed
description Plastome sequence data is most often extracted from plant whole genome sequencing data and need to be assembled and annotated separately from the nuclear genome sequence. In projects comprising multiple genomes, it is labour intense to individually process the plastomes as it requires many steps and software. This study developed Plastaumatic - an automated pipeline for both assembly and annotation of plastomes, with the scope of the researcher being able to load whole genome sequence data with minimal manual input, and therefore a faster runtime. The main structure of the current automated pipeline includes trimming of adaptor and low-quality sequences using fastp, de novo plastome assembly using NOVOPlasty, standardization and quality checking of the assembled genomes through a custom script utilizing BLAST+ and SAMtools, annotation of the assembled genomes using AnnoPlast, and finally generating the required files for NCBI GenBank submissions. The pipeline is demonstrated with 12 potato accessions and three soybean accessions.
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spelling pubmed-96696432022-11-18 Plastaumatic: Automating plastome assembly and annotation Chen, Wenyi Achakkagari, Sai Reddy Strömvik, Martina Front Plant Sci Plant Science Plastome sequence data is most often extracted from plant whole genome sequencing data and need to be assembled and annotated separately from the nuclear genome sequence. In projects comprising multiple genomes, it is labour intense to individually process the plastomes as it requires many steps and software. This study developed Plastaumatic - an automated pipeline for both assembly and annotation of plastomes, with the scope of the researcher being able to load whole genome sequence data with minimal manual input, and therefore a faster runtime. The main structure of the current automated pipeline includes trimming of adaptor and low-quality sequences using fastp, de novo plastome assembly using NOVOPlasty, standardization and quality checking of the assembled genomes through a custom script utilizing BLAST+ and SAMtools, annotation of the assembled genomes using AnnoPlast, and finally generating the required files for NCBI GenBank submissions. The pipeline is demonstrated with 12 potato accessions and three soybean accessions. Frontiers Media S.A. 2022-11-03 /pmc/articles/PMC9669643/ /pubmed/36407635 http://dx.doi.org/10.3389/fpls.2022.1011948 Text en Copyright © 2022 Chen, Achakkagari and Strömvik https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Chen, Wenyi
Achakkagari, Sai Reddy
Strömvik, Martina
Plastaumatic: Automating plastome assembly and annotation
title Plastaumatic: Automating plastome assembly and annotation
title_full Plastaumatic: Automating plastome assembly and annotation
title_fullStr Plastaumatic: Automating plastome assembly and annotation
title_full_unstemmed Plastaumatic: Automating plastome assembly and annotation
title_short Plastaumatic: Automating plastome assembly and annotation
title_sort plastaumatic: automating plastome assembly and annotation
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9669643/
https://www.ncbi.nlm.nih.gov/pubmed/36407635
http://dx.doi.org/10.3389/fpls.2022.1011948
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