Data

Drosophila serrata genome scaffolding and annotation

The University of Queensland
Dr Scott Allen (Aggregated by) Dr Scott Allen (Aggregated by) Professor Steve Chenoweth (Aggregated by) Professor Steve Chenoweth (Aggregated by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.48610/ce96855&rft.title=Drosophila serrata genome scaffolding and annotation&rft.identifier=RDM ID: 02979de6-e671-4d6a-895c-cc9d01e73822&rft.publisher=The University of Queensland&rft.description=Supplementary files required for https://github.com/scottlallen/DserSweepsThe reference genome of D. serrata was created using long-read sequencing technology and has a length of 198 Mbp and a contig N50 of 0.94 Mbp (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002093755.2/). We subsequently used Dovetail HiRise and Hi-C methods to scaffold those contigs and achieved a scaffold N50 of 30.3 Mb. The six largest scaffolds span 80% of the genome and reach near chromosome-arm level length except for 2L, which is spanned by two large scaffolds of 21Mb and 8.7 Mb. The genome was annotated by NCBI and lifted over to the Hi-C genome. File Descriptions:FASTA Files: drosophila_06Jul2018_A8VGg.fasta : Original Hi-C genome sequence. - drosophila_06Jul2018_A8VGg_noSpecialChar.fasta : Hi-C genome sequence with special characters removed from scaffold names.drosophila_06Jul2018_A8VGg_noSpecialChar_MASKED.fasta : Masked version of the Hi-C genome sequence. drosophila_06Jul2018_A8VGg_noSpecialChar_MASKED_shortName.fasta : Masked version of the Hi-C genome sequence with short scaffold names. - `top6.anc.fa : Hi-C genome sequence of the 6 longest scaffolds specifying the ancestral sequence. GFF Files: GCF_002093755.1_Dser1.0_genomic_OGcontigs_NOregion_HiC_liftOver_sorted.gff : NCBI Annotation file converted to Hi-C scaffolds. GCF_002093755.1_Dser1.0_genomic_OGcontigs_NOregion_HiC_liftOver_sorted_noSpecialChar.gff : Annotation file converted to Hi-C scaffolds with special characters removed from scaffold names. FAA File: GCF_002093755.1_Dser1.0_protein.faa : Protein sequences. FNA File: GCF_002093755.1_Dser1.0_rna_from_genomic.fna : Coding sequences.&rft.creator=Dr Scott Allen&rft.creator=Dr Scott Allen&rft.creator=Professor Steve Chenoweth&rft.creator=Professor Steve Chenoweth&rft.date=2024&rft_rights= http://guides.library.uq.edu.au/deposit_your_data/terms_and_conditions&rft_subject=eng&rft_subject=Genomics and transcriptomics&rft_subject=Bioinformatics and computational biology&rft_subject=BIOLOGICAL SCIENCES&rft_subject=Statistical and quantitative genetics&rft_subject=Biological adaptation&rft_subject=Evolutionary biology&rft_subject=Molecular evolution&rft_subject=Genetics&rft_subject=Deep learning&rft_subject=Machine learning&rft_subject=INFORMATION AND COMPUTING SCIENCES&rft_subject=Neural networks&rft.type=dataset&rft.language=English Access the data
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[email protected]
School of the Environment

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Supplementary files required for https://github.com/scottlallen/DserSweepsThe reference genome of D. serrata was created using long-read sequencing technology and has a length of 198 Mbp and a contig N50 of 0.94 Mbp (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002093755.2/). We subsequently used Dovetail HiRise and Hi-C methods to scaffold those contigs and achieved a scaffold N50 of 30.3 Mb. The six largest scaffolds span 80% of the genome and reach near chromosome-arm level length except for 2L, which is spanned by two large scaffolds of 21Mb and 8.7 Mb. The genome was annotated by NCBI and lifted over to the Hi-C genome. File Descriptions:FASTA Files: drosophila_06Jul2018_A8VGg.fasta : Original Hi-C genome sequence. - drosophila_06Jul2018_A8VGg_noSpecialChar.fasta : Hi-C genome sequence with special characters removed from scaffold names.drosophila_06Jul2018_A8VGg_noSpecialChar_MASKED.fasta : Masked version of the Hi-C genome sequence. drosophila_06Jul2018_A8VGg_noSpecialChar_MASKED_shortName.fasta : Masked version of the Hi-C genome sequence with short scaffold names. - `top6.anc.fa : Hi-C genome sequence of the 6 longest scaffolds specifying the ancestral sequence. GFF Files: GCF_002093755.1_Dser1.0_genomic_OGcontigs_NOregion_HiC_liftOver_sorted.gff : NCBI Annotation file converted to Hi-C scaffolds. GCF_002093755.1_Dser1.0_genomic_OGcontigs_NOregion_HiC_liftOver_sorted_noSpecialChar.gff : Annotation file converted to Hi-C scaffolds with special characters removed from scaffold names. FAA File: GCF_002093755.1_Dser1.0_protein.faa : Protein sequences. FNA File: GCF_002093755.1_Dser1.0_rna_from_genomic.fna : Coding sequences.

Issued: 23 07 2024

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Subjects
Biological Sciences | Bioinformatics and Computational Biology | Biological Adaptation | Deep Learning | Evolutionary Biology | Genetics | Genomics and Transcriptomics | Information and Computing Sciences | Machine Learning | Molecular Evolution | Neural Networks | Statistical and Quantitative Genetics | eng |

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Other Information
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach

local : UQ:5306efe

Wang, Yiguan, Allen, Scott L., Reddiex, Adam J. and Chenoweth, Stephen F. (2024). The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach. Molecular Ecology, 33 (18). doi: 10.1111/mec.17499

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