Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects
The emergence of third generation sequencing (3GS; long‐reads) is making closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of non‐model organisms. However, long‐read technologies result...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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Wiley
2020
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| _version_ | 1797093508536860672 |
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| author | Jaworski, C Allan, CW Matzkin, LM |
| author_facet | Jaworski, C Allan, CW Matzkin, LM |
| author_sort | Jaworski, C |
| collection | OXFORD |
| description | The emergence of third generation sequencing (3GS; long‐reads) is making closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of non‐model organisms. However, long‐read technologies result in higher sequencing error rates and therefore impose an elevated cost of sufficient coverage to achieve high enough quality. In this context, hybrid assemblies, combining short‐reads and long‐reads provide an alternative efficient and cost‐effective approach to generate de novo, chromosome‐level genome assemblies. The array of available software programs for hybrid genome assembly, sequence correction and manipulation are constantly being expanded and improved. This makes it difficult for non‐experts to find efficient, fast and tractable computational solutions for genome assembly, especially in the case of non‐model organisms lacking a reference genome or one from a closely related species. In this study, we review and test the most recent pipelines for hybrid assemblies, comparing the model organism Drosophila melanogaster to a non‐model cactophilic Drosophila, D. mojavensis. We show that it is possible to achieve excellent contiguity on this non‐model organism using the DBG2OLC pipeline. |
| first_indexed | 2024-03-07T04:01:29Z |
| format | Journal article |
| id | oxford-uuid:c4b9c902-3232-4fdb-8652-9bec62a3720d |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:01:29Z |
| publishDate | 2020 |
| publisher | Wiley |
| record_format | dspace |
| spelling | oxford-uuid:c4b9c902-3232-4fdb-8652-9bec62a3720d2022-03-27T06:25:39ZChromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insectsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c4b9c902-3232-4fdb-8652-9bec62a3720dEnglishSymplectic ElementsWiley2020Jaworski, CAllan, CWMatzkin, LMThe emergence of third generation sequencing (3GS; long‐reads) is making closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of non‐model organisms. However, long‐read technologies result in higher sequencing error rates and therefore impose an elevated cost of sufficient coverage to achieve high enough quality. In this context, hybrid assemblies, combining short‐reads and long‐reads provide an alternative efficient and cost‐effective approach to generate de novo, chromosome‐level genome assemblies. The array of available software programs for hybrid genome assembly, sequence correction and manipulation are constantly being expanded and improved. This makes it difficult for non‐experts to find efficient, fast and tractable computational solutions for genome assembly, especially in the case of non‐model organisms lacking a reference genome or one from a closely related species. In this study, we review and test the most recent pipelines for hybrid assemblies, comparing the model organism Drosophila melanogaster to a non‐model cactophilic Drosophila, D. mojavensis. We show that it is possible to achieve excellent contiguity on this non‐model organism using the DBG2OLC pipeline. |
| spellingShingle | Jaworski, C Allan, CW Matzkin, LM Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title | Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title_full | Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title_fullStr | Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title_full_unstemmed | Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title_short | Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects |
| title_sort | chromosome level hybrid de novo genome assemblies as an attainable option for non model insects |
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