<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[qiime2的物种注释研究]]></title><description><![CDATA[<p dir="auto"><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0470-z" rel="nofollow ugc">https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0470-z</a><br />
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin<br />
qiime2的分类器使用的是q2-feature-classifier插件 这个插件包括了如下几个功能：<br />
classify-consensus-blast        BLAST+ consensus taxonomy classifier<br />
classify-consensus-vsearch      VSEARCH-based consensus taxonomy classifier<br />
classify-hybrid-vsearch-sklearn ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</p>
<p dir="auto">classify-sklearn                Pre-fitted sklearn-based taxonomy classifier<br />
extract-reads                   Extract reads from reference sequences.<br />
fit-classifier-naive-bayes      Train the naive_bayes classifier<br />
fit-classifier-sklearn          Train an almost arbitrary scikit-learn classifier</p>
<p dir="auto">这些功能主要分为三类：<br />
1.基于机器学习的machine-learning<br />
2.基于对齐的alignment-based<br />
从代码看qiime的对齐方案用了blast+lca 和我们的病原的方案一样<br />
blast后面看看怎么优化<br />
3.构建相关的数据库</p>
]]></description><link>http://an.forum.genostack.com/topic/840/qiime2的物种注释研究</link><generator>RSS for Node</generator><lastBuildDate>Sat, 13 Jun 2026 12:34:31 GMT</lastBuildDate><atom:link href="http://an.forum.genostack.com/topic/840.rss" rel="self" type="application/rss+xml"/><pubDate>Wed, 12 Apr 2023 08:59:15 GMT</pubDate><ttl>60</ttl><item><title><![CDATA[Reply to qiime2的物种注释研究 on Wed, 12 Apr 2023 10:38:40 GMT]]></title><description><![CDATA[<p dir="auto">eDNA需要部署的流程和数据库：<br />
1.denoise+blast物种注释<br />
2.denoise+bayes物种注释<br />
3.nextflow 全流程<br />
<s>3.denoise+rdp物种注释（这个不需要 classify-sklearn和RDP类似）</s><br />
4.训练分类数据库:makeblastdb、qiime2_train<br />
5.BOLD数据库、NT数据库、mitofish、silva、unite<br />
6.qiime2的全流程<br />
7.交互式分析工具、blast server<br />
8.nextflow hifi 全长</p>
]]></description><link>http://an.forum.genostack.com/post/2032</link><guid isPermaLink="true">http://an.forum.genostack.com/post/2032</guid><dc:creator><![CDATA[anneng]]></dc:creator><pubDate>Wed, 12 Apr 2023 10:38:40 GMT</pubDate></item></channel></rss>