Feb2024 reference datasets for Mitohelper

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

Dec 2023 update: COI dataset was cleaned up in Dec2023 to remove non-COI 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.Feb2024.tsv (844,071 records)

mitofish.12S.Feb2024.tsv (55,390 records)

mitofish.12S.Feb2024_NR.fasta (FASTA file of 12S rRNA gene records)

mitofish.COI.Feb2024.tsv (308,857 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

适用于Mitohelper（https://github.com/aomlomics/mitohelper）的参考数据集（2024年2月更新版）

2023年12月更新说明：2023年12月对细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI）数据集完成清理，移除了非COI序列记录。

Mitohelper是一款专为鱼类环境DNA（environmental DNA, eDNA）研究打造的开源工具仓库，可助力实验设计、序列比对可视化及参考序列分析。有关数据库构建流程，请参阅我们的研究论文及Mitohelper的维基页面。

一、包含基因、分类学及序列信息的制表符分隔格式（tab-separated values, TSV）参考数据库文件：
1. mitofish.all.Feb2024.tsv（共844,071条记录）
2. mitofish.12S.Feb2024.tsv（共55,390条记录）
3. mitofish.12S.Feb2024_NR.fasta（12S核糖体RNA（ribosomal RNA, rRNA）基因记录的FASTA格式文件）
4. mitofish.COI.Feb2024.tsv（共308,857条记录）

二、去重复且兼容QIIME 2的12S/12S+16S+18S rRNA参考数据集：
1. 12S-seqs-derep-uniq.qza
2. 12S-tax-derep-uniq.qza
3. 12S-16S-18S-seqs.qza
4. 12S-16S-18S-tax.qza

若您使用Mitohelper，请引用以下文献：
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