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Published October 11, 2024 | Version v39
Dataset Open

Dec2024 reference datasets for Mitohelper

Authors/Creators

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

Description

Reference datasets (Dec 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.Dec2024.tsv (874,975 records)
  • mitofish.12S.Dec2024.tsv (60,610 records of 12S rRNA gene >50 bp long)
  • mitofish.12S.Dec2024_NR.fasta (FASTA file of 12S rRNA gene records)
  • mitofish.COI.Dec2024.tsv (318,682 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
md5:1b503669bcfdd7cae2ba68bb6e6f32e0
99.8 MB Download
md5:859adf69391026b54a2a89a2184c4598
7.6 MB Download
md5:3162ebda008af519e1cb7c8df7ae848e
2.7 MB Download
md5:076ea8238302142c5938d33bff6cacc8
835.3 kB Download
md5:210c4ad14bbc9a12d62b15d4dea31572
56.9 MB Download
md5:ef582157dc3595a77154c2267022741e
41.9 MB Download
md5:9df79a31777038c249399d89b1b589eb
1.5 GB Download
md5:34f0aa95cb9bd5d33a5b385e7fe32b37
585.5 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.