Dec2024 reference datasets for Mitohelper

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

用于Mitohelper（https://github.com/aomlomics/mitohelper）的参考数据集（2024年12月更新版）

Mitohelper是一个旨在助力鱼类环境DNA（environmental DNA, eDNA）研究中实验设计、序列比对可视化及参考序列分析的代码仓库。请参阅我们的论文及Mitohelper的维基页面以了解数据库构建流程。

I. 制表符分隔值（TSV）格式的参考数据库文件，包含基因、分类学及序列信息：

mitofish.all.Dec2024.tsv（共874,975条记录）
mitofish.12S.Dec2024.tsv（包含60,610条长度大于50 bp的12S核糖体RNA（ribosomal RNA, rRNA）基因记录）
mitofish.12S.Dec2024_NR.fasta（12S rRNA基因记录的FASTA格式文件）
mitofish.COI.Dec2024.tsv（共318,682条记录）

II. 去冗余的、兼容QIIME 2的12S/12S+16S+18S rRNA参考数据集：

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

若使用Mitohelper，请引用如下文献：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