https://doi.org/10.5061/dryad.g1jwstqzn

Overview:

This repository contains the data used in the study "Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness" by Hench et. al., which introduces the Antarctic fur seal reference genome version arcGaz4_h1.

The data set includes:

• the two initial de novo haplotype assemblies by Dovetail genomics (de_novo_genomes.tar.gz)
• the genome annotation of the final assembly for the first haplotype in two formats ("arcGaz4_h1", arcGaz4_h1_annotation.gff3.gz and arcGaz4_h1_annotation.gtf.gz)
• a multi-species whole genome alignment of eleven pinniped species (pinniped_set.hal)
• the inferred neutral tree for the eleven aligned species (rerooted.tree)
• a one-on-one whole genome alignment of the Antarctic fur seal and the California sea lion (slim_zalcal_v1_on_arcgaz_anc_h1.psl.gz)
• BUSCO scoring results for the genome arcGaz4_h1 (busco.tar.gz)
• evolutionary conservation scores estimated using gerp++ (gerp.tar.gz)
• genetic differentiation between the aligned otariid and phocid genomes (fst.tar.gz)
• description of the gene ontology information linked to the BUSCO genes as available at the time of analysis (go_terms.tar.gz)
• a summary of the conservation and differentiation scores within 50kb sliding windows with 25mb increments along arcGaz4_h1 (win_gerp_fst.tsv.gz)
• a summary of the conservation and differentiation scores per complete BUSCO gene within arcGaz4_h1 (busco_gerp_fst.tsv.gz)
• a inventory of all files, when unzipping the zipped folders (repo_content.txt)
• check-sums for all data files (md5.txt)
• this README file (readme.md)

[ dryad 21.56 GiB ]
├─ pinniped_set.hal       │ ███████████████████████████████████│  93%     20.07 GiB
├─ de_novo_genomes.tar.gz │                                   █│   6%      1.40 GiB
├─ gerp.tar.gz            │                                    │   0%     27.47 MiB
├─ slim_zalcal_v1_on_arcg │                                    │   0%     23.91 MiB
├─ fst.tar.gz             │                                    │   0%     17.13 MiB
├─ arcGaz4_h1_annotation. │                                    │   0%      5.16 MiB
├─ win_gerp_fst.tsv.gz    │                                    │   0%      4.55 MiB
├─ arcGaz4_h1_annotation. │                                    │   0%      3.76 MiB
├─ busco.tar.gz           │                                    │   0%      1.26 MiB
├─ busco_gerp_fst.tsv.gz  │                                    │   0%    774.47 KiB
├─ go_terms.tar.gz        │                                    │   0%    384.27 KiB
├─ repo_content.txt       │                                    │   0%      8.33 KiB
├─ readme.md              │                                    │   0%      4.81 KiB
├─ md5.txt                │                                    │   0%         705 B
└─ rerooted.tree          │                                    │   0%         309 B

The integrity of the files can be checked using the provided check-sums within the file md5.txt using the following unix command:

md5sum -c md5.txt

The folders can be un-compressed using the unix command tar, for example:

tar -xf gerp.tar.gz

File types:

After unpacking, most files are plain text files regardless of their suffix (eg .tsv, .psl) and can be read by any text editor like any other .txt file.
The (non-txt) suffix was kept for consistency between the analysis and the repository.
An exception to this is the multi-species alignment pinniped_set.hal, which is in the "Hierarchical Alignment Format" (hal).
See Hickey et al. (2013) for a detailed description of the hal format:

Hickey, G. et al. (2013). HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics, 29(10), 1341–1342. https://doi.org/10.1093/bioinformatics/btt128

Files that are gzip-compressed (that additionally contain a .gz suffix) can be un-compressed using the unix command gunzip, for example:

gunzip busco_gerp_fst.tsv.gz

Relevant software:

For reading the files:

• GNU gzip
• GNU tar

Software originally used within the analysis is documented using conda environments and apptainer containers.
For details, please refer to the accompanying code repository at Zenodo (s. below).

Sharing/Access information

In addition to this data repository, there exist two additional repositories linked to the same study:

• Analysis code is deposited at Zenodo at the repository 10.5281/zenodo.10979149
• The final genome assemblies are deposited at NCBI, under the accession numbers (PRJNA1099198, haplotype 1) and (PRJNA1099197, haplotype 2)