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Published July 18, 2024 | Version v35
Dataset Open

Jul2024 reference datasets for Mitohelper

Authors/Creators

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

Description

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

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.Jul2024.tsv (864,107 records)
  • mitofish.12S.Jul2024.tsv (60,281 records)
  • mitofish.12S.Jul2024_NR.fasta (FASTA file of 12S rRNA gene records)
  • mitofish.COI.Jul2024.tsv (312,741 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 Download all
md5:692d4be2d8046822e6f39ccb54216ac6
100.2 MB Download
md5:ae38e26d5e9f6a1dc4e51664a74acd29
7.6 MB Download
md5:f9642c21ae280b58b33112ff8271bb19
3.2 MB Download
md5:2e9ca006a6828172dd707e1859624759
828.1 kB Download
md5:7278e72e319f575c89ca90e4a0802b95
63.2 MB Download
md5:bcf93db9c37e015f034b860a44652488
48.2 MB Download
md5:268880472f1f1625836dad786d45e0a5
1.5 GB Download
md5:52b521014198f529f9e464b8d1e7935e
578.2 MB Download

Additional details

Related works

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

Dates

Updated
2023-04-23

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.