Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
Additional file 7. Results from parameter optimization for de novo assembly and genotyping. Eight parameter optimization series were conducted following Rochette & Catchen (2017) [45] to identify optimal parameters to genotype reduced representation sequencing (RRS) data with Stacks v2.4 (Rochet...
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ftsmithonian:oai:figshare.com:article/16305513 2023-05-15T18:25:30+02:00 Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing Henrik Christiansen (5717978) Franz M. Heindler (5717981) Bart Hellemans (3246426) Quentin Jossart (532157) Francesca Pasotti (5665906) Henri Robert (6970418) Marie Verheye (11309976) Bruno Danis (811532) Marc Kochzius (242381) Frederik Leliaert (186222) Camille Moreau (811531) Tasnim Patel (11309979) Anton P. Van de Putte (11309982) Ann Vanreusel (220781) Filip A. M. Volckaert (8140614) Isa Schön (153646) 2021-08-21T05:00:00Z https://doi.org/10.6084/m9.figshare.16305513.v1 unknown https://figshare.com/articles/journal_contribution/Additional_file_7_of_Facilitating_population_genomics_of_non-model_organisms_through_optimized_experimental_design_for_reduced_representation_sequencing/16305513 doi:10.6084/m9.figshare.16305513.v1 CC BY + CC0 CC0 CC-BY Genetics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Text Journal contribution 2021 ftsmithonian https://doi.org/10.6084/m9.figshare.16305513.v1 2021-12-20T03:49:57Z Additional file 7. Results from parameter optimization for de novo assembly and genotyping. Eight parameter optimization series were conducted following Rochette & Catchen (2017) [45] to identify optimal parameters to genotype reduced representation sequencing (RRS) data with Stacks v2.4 (Rochette et al. 2019) [21]; one test series for each species/species complex. The Stacks parameter m was kept constant (m = 3), while parameters M and n were varied together from 1 to 9. Subsequently, only loci present in 80% of the samples were retained and for each M = n parameter the number of loci and polymorphic loci was plotted, as well as the proportion of these loci containing 0 to 10 or > 10 SNPs. In ostracods, the library contained DNA from a species-complex, resulting in very few shared loci across 80% of the samples. Therefore, in this case results based on loci shared by 50% of samples are shown. Optimal M = n values were decided in all cases with this information (and reported in Table 5). Note, however, that it is impossible to make absolute calls regarding the ideal value. Other Non-Article Part of Journal/Newspaper Southern Ocean Unknown Southern Ocean |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
ftsmithonian |
language |
unknown |
topic |
Genetics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
spellingShingle |
Genetics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean Henrik Christiansen (5717978) Franz M. Heindler (5717981) Bart Hellemans (3246426) Quentin Jossart (532157) Francesca Pasotti (5665906) Henri Robert (6970418) Marie Verheye (11309976) Bruno Danis (811532) Marc Kochzius (242381) Frederik Leliaert (186222) Camille Moreau (811531) Tasnim Patel (11309979) Anton P. Van de Putte (11309982) Ann Vanreusel (220781) Filip A. M. Volckaert (8140614) Isa Schön (153646) Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
topic_facet |
Genetics Biodiversity Genome scan Genotyping by sequencing In silico digestion RADseq Southern Ocean |
description |
Additional file 7. Results from parameter optimization for de novo assembly and genotyping. Eight parameter optimization series were conducted following Rochette & Catchen (2017) [45] to identify optimal parameters to genotype reduced representation sequencing (RRS) data with Stacks v2.4 (Rochette et al. 2019) [21]; one test series for each species/species complex. The Stacks parameter m was kept constant (m = 3), while parameters M and n were varied together from 1 to 9. Subsequently, only loci present in 80% of the samples were retained and for each M = n parameter the number of loci and polymorphic loci was plotted, as well as the proportion of these loci containing 0 to 10 or > 10 SNPs. In ostracods, the library contained DNA from a species-complex, resulting in very few shared loci across 80% of the samples. Therefore, in this case results based on loci shared by 50% of samples are shown. Optimal M = n values were decided in all cases with this information (and reported in Table 5). Note, however, that it is impossible to make absolute calls regarding the ideal value. |
format |
Other Non-Article Part of Journal/Newspaper |
author |
Henrik Christiansen (5717978) Franz M. Heindler (5717981) Bart Hellemans (3246426) Quentin Jossart (532157) Francesca Pasotti (5665906) Henri Robert (6970418) Marie Verheye (11309976) Bruno Danis (811532) Marc Kochzius (242381) Frederik Leliaert (186222) Camille Moreau (811531) Tasnim Patel (11309979) Anton P. Van de Putte (11309982) Ann Vanreusel (220781) Filip A. M. Volckaert (8140614) Isa Schön (153646) |
author_facet |
Henrik Christiansen (5717978) Franz M. Heindler (5717981) Bart Hellemans (3246426) Quentin Jossart (532157) Francesca Pasotti (5665906) Henri Robert (6970418) Marie Verheye (11309976) Bruno Danis (811532) Marc Kochzius (242381) Frederik Leliaert (186222) Camille Moreau (811531) Tasnim Patel (11309979) Anton P. Van de Putte (11309982) Ann Vanreusel (220781) Filip A. M. Volckaert (8140614) Isa Schön (153646) |
author_sort |
Henrik Christiansen (5717978) |
title |
Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_short |
Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_full |
Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_fullStr |
Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_full_unstemmed |
Additional file 7 of Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
title_sort |
additional file 7 of facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing |
publishDate |
2021 |
url |
https://doi.org/10.6084/m9.figshare.16305513.v1 |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_relation |
https://figshare.com/articles/journal_contribution/Additional_file_7_of_Facilitating_population_genomics_of_non-model_organisms_through_optimized_experimental_design_for_reduced_representation_sequencing/16305513 doi:10.6084/m9.figshare.16305513.v1 |
op_rights |
CC BY + CC0 |
op_rightsnorm |
CC0 CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.16305513.v1 |
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1766206992363290624 |