Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits
Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, w...
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2021
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crwinnower:10.22541/au.162605765.53212369/v1 2024-06-02T08:03:11+00:00 Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits Mena, Belen Jimenez Flávio, Hugo Henriques, Romina Manuzzi, Alice Ramos, Miguel Meldrup, Dorte Edson, Janette Palsson, Snaebjorn Ólafsdóttir, Guðbjörg Ásta Ovenden, Jennifer Nielsen, Einar 2021 http://dx.doi.org/10.22541/au.162605765.53212369/v1 unknown Authorea, Inc. posted-content 2021 crwinnower https://doi.org/10.22541/au.162605765.53212369/v1 2024-05-07T14:19:25Z Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompass our considerations and guidelines for bait design to benefit researchers and practitioners. The supeRbaits R package is user‐friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits Other/Unknown Material atlantic cod Atlantic salmon The Winnower |
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Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompass our considerations and guidelines for bait design to benefit researchers and practitioners. The supeRbaits R package is user‐friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits |
format |
Other/Unknown Material |
author |
Mena, Belen Jimenez Flávio, Hugo Henriques, Romina Manuzzi, Alice Ramos, Miguel Meldrup, Dorte Edson, Janette Palsson, Snaebjorn Ólafsdóttir, Guðbjörg Ásta Ovenden, Jennifer Nielsen, Einar |
spellingShingle |
Mena, Belen Jimenez Flávio, Hugo Henriques, Romina Manuzzi, Alice Ramos, Miguel Meldrup, Dorte Edson, Janette Palsson, Snaebjorn Ólafsdóttir, Guðbjörg Ásta Ovenden, Jennifer Nielsen, Einar Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
author_facet |
Mena, Belen Jimenez Flávio, Hugo Henriques, Romina Manuzzi, Alice Ramos, Miguel Meldrup, Dorte Edson, Janette Palsson, Snaebjorn Ólafsdóttir, Guðbjörg Ásta Ovenden, Jennifer Nielsen, Einar |
author_sort |
Mena, Belen Jimenez |
title |
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
title_short |
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
title_full |
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
title_fullStr |
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
title_full_unstemmed |
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits |
title_sort |
fishing for dna? designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool superbaits |
publisher |
Authorea, Inc. |
publishDate |
2021 |
url |
http://dx.doi.org/10.22541/au.162605765.53212369/v1 |
genre |
atlantic cod Atlantic salmon |
genre_facet |
atlantic cod Atlantic salmon |
op_doi |
https://doi.org/10.22541/au.162605765.53212369/v1 |
_version_ |
1800747663980756992 |