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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-9669643 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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