Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species
Genotype-by-sequencing (GBS) is a widely used cost-effective technique to obtain large numbers of genetic markers from populations. Although a standard reference-based pipeline can be followed to analyze these reads, a reference genome is still not available for a large number of species. Hence,...
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| Formato: | article |
| Lenguaje: | Inglés |
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Cold Sprimg Harbor Laboratory (CSH)
2024
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| Acceso en línea: | https://www.biorxiv.org/content/10.1101/2020.11.28.402131v1 http://hdl.handle.net/20.500.12324/39793 https://doi.org/10.1101/2020.11.28.402131 |
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RepoAGROSAVIA39793 |
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dspace |
| institution |
Corporación Colombiana de Investigación Agropecuaria |
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Repositorio AGROSAVIA |
| language |
Inglés |
| topic |
Investigación agropecuaria - A50 Análisis de datos Método estadístico Genómica Transversal http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_92382 |
| spellingShingle |
Investigación agropecuaria - A50 Análisis de datos Método estadístico Genómica Transversal http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_92382 Parra Salazar, Andrea Gomez, Jorge Lozano Arce, Daniela Reyes Herrera, Paula H. Duitama, Jorge Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| description |
Genotype-by-sequencing (GBS) is a widely used cost-effective technique
to obtain large numbers of genetic markers from populations. Although
a standard reference-based pipeline can be followed to analyze these reads, a
reference genome is still not available for a large number of species. Hence, several
research groups require reference-free approaches to generate the genetic
variability information that can be obtained from a GBS experiment. Unfortunately,
tools to perform de-novo analysis of GBS reads are scarce and some of
the existing solutions are difficult to operate under different settings generated by
the existing GBS protocols. In this manuscript we describe a novel algorithm to
perform reference-free variants detection and genotyping from GBS reads. Nonexact
searches on a dynamic hash table of consensus sequences allow to perform
efficient read clustering and sorting. This algorithm was integrated in the Next
Generation Sequencing Experience Platform (NGSEP) to integrate the state-ofthe-
art variants detector already implemented in this tool. We performed benchmark
experiments with three different real populations of plants and animals with
different structures and ploidies, and sequenced with different GBS protocols at
different read depths. These experiments show that NGSEP has comparable and
in some cases better accuracy and always better computational efficiency compared
to existing solutions. We expect that this new development will be useful
for several research groups conducting population genetic studies in a wide variety
of species. |
| format |
article |
| author |
Parra Salazar, Andrea Gomez, Jorge Lozano Arce, Daniela Reyes Herrera, Paula H. Duitama, Jorge |
| author_facet |
Parra Salazar, Andrea Gomez, Jorge Lozano Arce, Daniela Reyes Herrera, Paula H. Duitama, Jorge |
| author_sort |
Parra Salazar, Andrea |
| title |
Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| title_short |
Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| title_full |
Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| title_fullStr |
Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| title_full_unstemmed |
Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species |
| title_sort |
robust and efficient software for reference-free genomic diversity analysis of gbs data on diploid and polyploid species |
| publisher |
Cold Sprimg Harbor Laboratory (CSH) |
| publishDate |
2024 |
| url |
https://www.biorxiv.org/content/10.1101/2020.11.28.402131v1 http://hdl.handle.net/20.500.12324/39793 https://doi.org/10.1101/2020.11.28.402131 |
| work_keys_str_mv |
AT parrasalazarandrea robustandefficientsoftwareforreferencefreegenomicdiversityanalysisofgbsdataondiploidandpolyploidspecies AT gomezjorge robustandefficientsoftwareforreferencefreegenomicdiversityanalysisofgbsdataondiploidandpolyploidspecies AT lozanoarcedaniela robustandefficientsoftwareforreferencefreegenomicdiversityanalysisofgbsdataondiploidandpolyploidspecies AT reyesherrerapaulah robustandefficientsoftwareforreferencefreegenomicdiversityanalysisofgbsdataondiploidandpolyploidspecies AT duitamajorge robustandefficientsoftwareforreferencefreegenomicdiversityanalysisofgbsdataondiploidandpolyploidspecies |
| _version_ |
1808105490899533824 |
| spelling |
RepoAGROSAVIA397932024-08-06T03:00:51Z Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species Parra Salazar, Andrea Gomez, Jorge Lozano Arce, Daniela Reyes Herrera, Paula H. Duitama, Jorge Investigación agropecuaria - A50 Análisis de datos Método estadístico Genómica Transversal http://aims.fao.org/aos/agrovoc/c_15962 http://aims.fao.org/aos/agrovoc/c_7377 http://aims.fao.org/aos/agrovoc/c_92382 Genotype-by-sequencing (GBS) is a widely used cost-effective technique to obtain large numbers of genetic markers from populations. Although a standard reference-based pipeline can be followed to analyze these reads, a reference genome is still not available for a large number of species. Hence, several research groups require reference-free approaches to generate the genetic variability information that can be obtained from a GBS experiment. Unfortunately, tools to perform de-novo analysis of GBS reads are scarce and some of the existing solutions are difficult to operate under different settings generated by the existing GBS protocols. In this manuscript we describe a novel algorithm to perform reference-free variants detection and genotyping from GBS reads. Nonexact searches on a dynamic hash table of consensus sequences allow to perform efficient read clustering and sorting. This algorithm was integrated in the Next Generation Sequencing Experience Platform (NGSEP) to integrate the state-ofthe- art variants detector already implemented in this tool. We performed benchmark experiments with three different real populations of plants and animals with different structures and ploidies, and sequenced with different GBS protocols at different read depths. These experiments show that NGSEP has comparable and in some cases better accuracy and always better computational efficiency compared to existing solutions. We expect that this new development will be useful for several research groups conducting population genetic studies in a wide variety of species. Corporación Colombiana de Investigación Agropecuaria - (AGROSAVIA) Universidad de los Andes (ULA) 2024-08-05T20:29:56Z 2024-08-05T20:29:56Z 2020-11-28 2020 article Artículo científico http://purl.org/coar/resource_type/c_2df8fbb1 info:eu-repo/semantics/article https://purl.org/redcol/resource_type/ART http://purl.org/coar/version/c_970fb48d4fbd8a85 https://www.biorxiv.org/content/10.1101/2020.11.28.402131v1 http://hdl.handle.net/20.500.12324/39793 https://doi.org/10.1101/2020.11.28.402131 reponame:Biblioteca Digital Agropecuaria de Colombia instname:Corporación colombiana de investigación agropecuaria AGROSAVIA eng BioRxiv 1 20 Kimberly R. Andrews, Jeffrey M. Good, Michael R. 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