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Published November 3, 2022 | Version Nov2022
Dataset Open

Nov2022 reference datasets for Mitohelper

Authors/Creators

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

Description

Reference datasets (Nov2022 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.Nov2022.tsv (776,210 records)
  • mitofish.12S.Nov2022.tsv (44,560 records)
  • mitofish.12S.Nov2022_NR.fasta (fasta file of 12S rRNA gene records)
  • mitofish.COI.Nov2022.tsv (314,143 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

Notes

Major update: The 12S rRNA gene sequence dataset is now filtered to only contain mitochondrial genomes annotated with 12S rRNA gene sequences. Sequences of the 12S rRNA gene are now extracted from complete mitochondrial genomes to construct a more gene-specific 12S rRNA dataset. 12S rRNA gene sequences in mitohelper's dataset are available for download as mitofish.12S.Nov2022_NR.fasta

Files

Files (2.1 GB)

Name Size
md5:1f7b75450ddfea75eca8e9c9f87eebc7
99.5 MB Download
md5:679437b4eec88346240fd4b362a31be1
7.4 MB Download
md5:026eafff5cd0b00077076e1d0abe8f02
2.4 MB Download
md5:3932d7083e162822d48d43762a8fd0ad
645.0 kB Download
md5:68d6d503312cffe7e5e6eaf9d9333baf
45.4 MB Download
md5:5f62a898d3e30b3c6375eb3a363ca378
33.5 MB Download
md5:a142f5553b6b72ae5fa0cbe981859562
1.3 GB Download
md5:873fdafd131d6de139cea9dbb4519663
599.0 MB Download