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Published September 10, 2024 | Version v37
Dataset Open

Sep2024 reference datasets for Mitohelper

Authors/Creators

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

Description

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

Sep 2024 Update: Double-checked long (>1,000 bp) 12S rRNA sequences and removed flanking non-12S sequences from some 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.Sep2024.tsv (870,372 records)
  • mitofish.12S.Sep2024.tsv (60,501 records)
  • mitofish.12S.Sep2024_NR.fasta (FASTA file of 12S rRNA gene records)
  • mitofish.COI.Sep2024.tsv (316,251 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)

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md5:30b822b11242d78bd8680537ad14b3e7
99.8 MB Download
md5:fb25c898e03a2efae4f81c41122f00ed
7.6 MB Download
md5:8f0c95a0e25b5f05ca8ca774649c68a7
2.7 MB Download
md5:c27ea89eb346e40ec75945359ce68014
830.4 kB Download
md5:5c966ff8ff60128c6a0e9e64c02da2a3
56.7 MB Download
md5:7d9b1433eb0b34775594321008810cac
41.7 MB Download
md5:34ec38dab6f1625d1fa07b02cb3b9c41
1.5 GB Download
md5:8dcf74f44c33f9ec15cc1e23d59c12df
582.1 MB Download

Additional details

Identifiers

DOI
10.1002/edn3.187

Related works

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

Dates

Accepted
2021-02-21
Publication date

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.