GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing
The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstr...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2023-12-01
|
| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/3973 |
| _version_ | 1797213945466978304 |
|---|---|
| author | A. Y. Pronozin E. A. Salina D. A. Afonnikov |
| author_facet | A. Y. Pronozin E. A. Salina D. A. Afonnikov |
| author_sort | A. Y. Pronozin |
| collection | DOAJ |
| description | The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutio nary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples). |
| first_indexed | 2024-03-07T16:04:05Z |
| format | Article |
| id | doaj.art-60b3953848684ccf8b34bd68d02f67ce |
| institution | Directory Open Access Journal |
| issn | 2500-3259 |
| language | English |
| last_indexed | 2024-04-24T11:06:20Z |
| publishDate | 2023-12-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj.art-60b3953848684ccf8b34bd68d02f67ce2024-04-11T15:31:06ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592023-12-0127773774510.18699/VJGB-23-861401GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencingA. Y. Pronozin0E. A. Salina1D. A. Afonnikov2Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS; Novosibirsk State Agrarian UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS; Novosibirsk State Agrarian University; Novosibirsk State UniversityThe development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutio nary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples).https://vavilov.elpub.ru/jour/article/view/3973genotyping by sequencing (gbs)bioinformatic pipelinehordeum |
| spellingShingle | A. Y. Pronozin E. A. Salina D. A. Afonnikov GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing Вавиловский журнал генетики и селекции genotyping by sequencing (gbs) bioinformatic pipeline hordeum |
| title | GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| title_full | GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| title_fullStr | GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| title_full_unstemmed | GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| title_short | GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| title_sort | gbs dp a bioinformatics pipeline for processing data coming from genotyping by sequencing |
| topic | genotyping by sequencing (gbs) bioinformatic pipeline hordeum |
| url | https://vavilov.elpub.ru/jour/article/view/3973 |
| work_keys_str_mv | AT aypronozin gbsdpabioinformaticspipelineforprocessingdatacomingfromgenotypingbysequencing AT easalina gbsdpabioinformaticspipelineforprocessingdatacomingfromgenotypingbysequencing AT daafonnikov gbsdpabioinformaticspipelineforprocessingdatacomingfromgenotypingbysequencing |