Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose...
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ftdatacite:10.6084/m9.figshare.8222156 2023-05-15T17:59:42+02:00 Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species Wright, Belinda Farquharson, Katherine McLennan, Elspeth Belov, Katherine Hogg, Carolyn Grueber, Catherine 2019 https://dx.doi.org/10.6084/m9.figshare.8222156 https://springernature.figshare.com/articles/Additional_file_1_of_From_reference_genomes_to_population_genomics_comparing_three_reference-aligned_reduced-representation_sequencing_pipelines_in_two_wildlife_species/8222156 unknown figshare https://dx.doi.org/10.1186/s12864-019-5806-y Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Genetics FOS Biological sciences Evolutionary Biology 69999 Biological Sciences not elsewhere classified 80699 Information Systems not elsewhere classified FOS Computer and information sciences 110309 Infectious Diseases FOS Health sciences dataset Dataset 2019 ftdatacite https://doi.org/10.6084/m9.figshare.8222156 https://doi.org/10.1186/s12864-019-5806-y 2021-11-05T12:55:41Z Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose (N = 40). Figure S1. Ratios of genotype calls between the three different pipelines for devils and geese. Figure S2. Venn diagram depicting number of shared loci between the three different pipelines for (a) devil and (b) goose. Figure S3. PCoA of the devil dataset only for the three pipelines, considering all three populations. Row one shows data processed with a call rate of 70%, row two shows data processed less stringently with a call rate of 30%. Figure S4. PCoAs of the two datasets after processing through three pipelines filtered less stringently, allowing more missing data (30% call rate). Figure S5. a) Gel image example of sample quality from 1 (highest) to 8 (no apparent DNA); b) - d) Gel quality rank (rank 7 and 8 not included as too low quality to include in study) vs. the amount of missing data of a sample for the b) Stacks, c) SAMtools and d) GATK pipelines. (ZIP 346 kb) Dataset Pink-footed Goose DataCite Metadata Store (German National Library of Science and Technology) Venn ENVELOPE(9.281,9.281,63.350,63.350) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Evolutionary Biology 69999 Biological Sciences not elsewhere classified 80699 Information Systems not elsewhere classified FOS Computer and information sciences 110309 Infectious Diseases FOS Health sciences |
spellingShingle |
Genetics FOS Biological sciences Evolutionary Biology 69999 Biological Sciences not elsewhere classified 80699 Information Systems not elsewhere classified FOS Computer and information sciences 110309 Infectious Diseases FOS Health sciences Wright, Belinda Farquharson, Katherine McLennan, Elspeth Belov, Katherine Hogg, Carolyn Grueber, Catherine Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
topic_facet |
Genetics FOS Biological sciences Evolutionary Biology 69999 Biological Sciences not elsewhere classified 80699 Information Systems not elsewhere classified FOS Computer and information sciences 110309 Infectious Diseases FOS Health sciences |
description |
Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose (N = 40). Figure S1. Ratios of genotype calls between the three different pipelines for devils and geese. Figure S2. Venn diagram depicting number of shared loci between the three different pipelines for (a) devil and (b) goose. Figure S3. PCoA of the devil dataset only for the three pipelines, considering all three populations. Row one shows data processed with a call rate of 70%, row two shows data processed less stringently with a call rate of 30%. Figure S4. PCoAs of the two datasets after processing through three pipelines filtered less stringently, allowing more missing data (30% call rate). Figure S5. a) Gel image example of sample quality from 1 (highest) to 8 (no apparent DNA); b) - d) Gel quality rank (rank 7 and 8 not included as too low quality to include in study) vs. the amount of missing data of a sample for the b) Stacks, c) SAMtools and d) GATK pipelines. (ZIP 346 kb) |
format |
Dataset |
author |
Wright, Belinda Farquharson, Katherine McLennan, Elspeth Belov, Katherine Hogg, Carolyn Grueber, Catherine |
author_facet |
Wright, Belinda Farquharson, Katherine McLennan, Elspeth Belov, Katherine Hogg, Carolyn Grueber, Catherine |
author_sort |
Wright, Belinda |
title |
Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
title_short |
Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
title_full |
Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
title_fullStr |
Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
title_full_unstemmed |
Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
title_sort |
additional file 1: of from reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species |
publisher |
figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.8222156 https://springernature.figshare.com/articles/Additional_file_1_of_From_reference_genomes_to_population_genomics_comparing_three_reference-aligned_reduced-representation_sequencing_pipelines_in_two_wildlife_species/8222156 |
long_lat |
ENVELOPE(9.281,9.281,63.350,63.350) |
geographic |
Venn |
geographic_facet |
Venn |
genre |
Pink-footed Goose |
genre_facet |
Pink-footed Goose |
op_relation |
https://dx.doi.org/10.1186/s12864-019-5806-y |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.8222156 https://doi.org/10.1186/s12864-019-5806-y |
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1766168585438232576 |