Microbiome.md

Microbiome

16s和宏基因组相关资料

Packages

• https://chiliubio.github.io/microeco_tutorial/

报告

• chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://www.omicstudio.cn/ueditor/php/upload/file/20200430/59416S%20rDNA%E6%B5%8B%E5%BA%8F%E5%88%86%E6%9E%90%E6%8A%A5%E5%91%8A%E4%B8%AD%E6%96%87%E5%B7%A5%E4%B8%9A%E7%89%88.pdf
• chrome-extension://mhnlakgilnojmhinhkckjpncpbhabphi/pages/pdf/web/viewer.html?file=https%3A%2F%2Fwww.omicstudio.cn%2Fueditor%2Fphp%2Fupload%2Ffile%2F20200430%2F59416S%2520rDNA%25E6%25B5%258B%25E5%25BA%258F%25E5%2588%2586%25E6%259E%2590%25E6%258A%25A5%25E5%2591%258A%25E4%25B8%25AD%25E6%2596%2587%25E5%25B7%25A5%25E4%25B8%259A%25E7%2589%2588.pdf#page=21&zoom=auto,-274,531

教程

• https://carpentries-lab.github.io/metagenomics-analysis/10-OtherResources/index.html 宏基因的详细教程
• 刘永鑫教程 https://github.com/YongxinLiu/Liu2020ProteinCell/tree/master
• Data Processing and Visualization for Metagenomics

WDL

• 平台使用的宏基因WDL流程 https://github.com/biobakery/biobakery_workflows
• EBI出版的分析笔记 https://github.com/EBI-Metagenomics/notebooks/tree/main

数据库

• GreenGenes

http://ftp.microbio.me/greengenes_release/2022.10/.

McDonald, D. et al. Greengenes2 enables a shared data universe for microbiome studies. bioRxiv (2022). https://doi.org/10.1101/2022.12.19.520774

    .

• Silva

https://www.arb-silva.de/.

"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Gl?ckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Opens external link in new windowNucl. Acids Res. 41 (D1): D590-D596.

• RDP

http://rdp.cme.msu.edu/.

Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM; Ribosomal Database Project. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 2003 Jan 1;31(1):442-3. doi: 10.1093/nar/gkg039

    .

• PR2

https://pr2-database.org/.

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597?C604.

• Unite

https://unite.ut.ee/.

Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Gl?ckner FO, Tedersoo L, Saar I, K?ljalg U, Abarenkov K. 2018. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, DOI: 10.1093/nar/gky1022

• BOLD

http://www.boldsystems.org/.

Ratnasingham S, Hebert PD. bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes. 2007 May 1;7(3):355-364. doi: 10.1111/j.1471-8286.2007.01678.x

• 12S

https://zenodo.org/record/7925541.

Jean Lim, S, Thompson, LR. Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies. Environmental DNA. 2021; 00: 1?C 10. https://doi.org/10.1002/edn3.187