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Published February 13, 2023 | Version v32
Dataset Open

Feb2024 reference datasets for Mitohelper

Authors/Creators

  • 1. University of Miami
  • 2. Mississippi State University

Description

Reference datasets (Feb 2024 update) for Mitohelper (https://github.com/aomlomics/mitohelper)

Dec 2023 update: COI dataset was cleaned up in Dec2023 to remove non-COI records.

Mitohelper is a repository built to facilitate experimental design, alignment visualization, and reference sequence analysis in fish eDNA studies. Refer to our paper and Mitohelper's wiki for database construction pipeline.

I. Reference database files in tab-separated format, containing gene, taxonomy, and sequence information:

  • mitofish.all.Feb2024.tsv (844,071 records)
  • mitofish.12S.Feb2024.tsv (55,390 records)
  • mitofish.12S.Feb2024_NR.fasta (FASTA file of 12S rRNA gene records)
  • mitofish.COI.Feb2024.tsv (308,857 records)

II. De-replicated QIIME 2-compatible 12S/12S+16S+18S rRNA reference datasets:

  • 12S-seqs-derep-uniq.qza
  • 12S-tax-derep-uniq.qza
  • 12S-16S-18S-seqs.qza
  • 12S-16S-18S-tax.qza

If you use Mitohelper, please cite:
Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1– 10.  https://doi.org/10.1002/edn3.187

Files

Files (2.3 GB)

Name Size
md5:7a9f9691fa0eb3f3a2e98fb9ed1a5d9d
99.9 MB Download
md5:b7117e6e873eb65dbb9e5ad9b89e7d37
7.5 MB Download
md5:815ae8f30e932149c8d38f8df24c2481
2.8 MB Download
md5:b72829904082c8e3c5b80372e4c2c1d4
751.0 kB Download
md5:6abda367d80be2b7398e6c2364a74562
57.6 MB Download
md5:99ef0eb066e7e21a6ac35c28de3635b8
43.5 MB Download
md5:d8fcecf61ff6cbc0b76440234e6832f4
1.5 GB Download
md5:65acc1eca4a29789cfac3a6535222884
612.6 MB Download

Additional details

Related works

Is published in
Publication: 10.1002/edn3.187 (DOI)

Dates

Updated
2023-02-13

Software

Repository URL
https://github.com/aomlomics/mitohelper

References

  • Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1– 10.