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<a href="/2024/07/13/metaspades/" target="_self">
MetaSPAdes: 最全能的宏基因组组装工具
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<a class="index-excerpt index-excerpt__noimg" href="/2024/07/13/metaspades/" target="_self">
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软件简介SPAdes是基因组组装的经典工具之一。这里我们所说的metaSPAdes，是SPAdes所提供的宏基因组组装模式。与megahit类似，它的原理同样是基于k-mer迭代的德布莱英图方法。在各种组装工具的评测论文中（如：Assembling metagenomes, one community at a time (BMC Genomics); Practical evaluation
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<time datetime="2024-07-13 15:20" pubdate>
2024-07-13
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<a href="/categories/Bioinformatics-tool/" class="category-chain-item">Bioinformatics tool</a>
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<a href="/2024/06/24/ai-chatbot-01/" target="_self">
Nature | Three ways ChatGPT helps me in my academic writing
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<a class="index-excerpt index-excerpt__noimg" href="/2024/06/24/ai-chatbot-01/" target="_self">
<div>
Nature的CAREER COLUMN栏目在2024年4月8日发布了一篇短文，是一位学者Dritjon Gruda分享自己使用AI的一些经验。其中有一些他提供的典型提示语模板，用于润色论文、审稿等，非常有用，记录下来。 润色学术写作 （Polishing academic writing）上下文（Context）是让GPT（甚至是任何人或者物）做出精确回答的关键。 When you’re us
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<time datetime="2024-06-24 13:26" pubdate>
2024-06-24
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<a href="/categories/AI-Techniques/" class="category-chain-item">AI Techniques</a>
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<h2 class="index-header">
<a href="/2024/02/28/megahit/" target="_self">
Megahit: 高效迅速的metagenome assembler
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</h2>
<a class="index-excerpt index-excerpt__noimg" href="/2024/02/28/megahit/" target="_self">
<div>
软件简介Megahit是基因组组装方面最常用且高效的软件之一。它主要的原理是基于k-mer迭代的德布莱英图方法。关于对德布莱英图的初步解读我写在另一篇blog(基于德布莱英图（De Bruijn graph）的宏基因组de novo拼接)里面。 在我的宏基因组数据处理中，megahit是和metaSPAdes、IDBA-UD等软件一起常被用到的，对我来说，它的主要优势是速度快、且占用运存小。我在运
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<time datetime="2024-02-28 10:53" pubdate>
2024-02-28
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<span class="category-chains">
<span class="category-chain">
<a href="/categories/Bioinformatics-tool/" class="category-chain-item">Bioinformatics tool</a>
</span>
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</article>
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<h2 class="index-header">
<a href="/2024/02/26/de-bruijn-graph/" target="_self">
基于德布莱英图（De Bruijn graph）的宏基因组de novo拼接
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</h2>
<a class="index-excerpt index-excerpt__noimg" href="/2024/02/26/de-bruijn-graph/" target="_self">
<div>
最近在做一批宏基因组数据的拼接工作，这里的拼接主要指从Read到Contig这个水平。然后因为是第一次做，有很多没懂的地方，在学习和实践的过程中，总结了一下。写成几篇博客记录一下，以后又不清楚了可以回来看一下。这篇博客主要记录一下宏基因组拼接的算法之一——基于德布莱英图（De Bruijn graph）的方法。 一、为什么使用德布莱英图？对于短序列read的拼接有两种基本算法，一种是基于Overl
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<time datetime="2024-02-26 15:28" pubdate>
2024-02-26
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<span class="category-chain">
<a href="/categories/Bioinformatics-tool/" class="category-chain-item">Bioinformatics tool</a>
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<a href="/2024/01/30/clumpify/" target="_self">
Clumpify.sh (from BBMap): Remove PCR Duplicates
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</h2>
<a class="index-excerpt index-excerpt__noimg" href="/2024/01/30/clumpify/" target="_self">
<div>
软件简介clumpify.sh实际上是BBMap工具中的一个脚本，本来的作用是去除重复序列。在宏基因组数据处理中，经常用于二代数据（经PCR建库）后的去除PCR重复。 去除PCR重复这本事是一件挺具有争议性的话题。首先，决定你到底需不需要做这一步的一个最重要的因素是要去调查清楚你的测序建库方法到底是不是PCR-free的，如果不是，才有做这一步的意义。另外，有相关的分析表明，PCR duplica
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<time datetime="2024-01-30 13:58" pubdate>
2024-01-30
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<a href="/categories/Bioinformatics-tool/" class="category-chain-item">Bioinformatics tool</a>
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<a href="/2024/01/26/trimmomatic/" target="_self">
Trimmomatic: Reads Quality Control
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</h2>
<a class="index-excerpt index-excerpt__noimg" href="/2024/01/26/trimmomatic/" target="_self">
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软件简介主要用于Illumina双端或单端测序数据的质控，基本原理是Sliding window。二代测序的扩增子测序和宏基因组测序用该方法都是可行的，我主要用来做宏基因组测序数据的质控。 参数列表ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.SLIDINGWINDOW: Perform
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<time datetime="2024-01-26 15:51" pubdate>
2024-01-26
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<a href="/categories/Bioinformatics-tool/" class="category-chain-item">Bioinformatics tool</a>
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<h2 class="index-header">
<a href="/2023/11/25/pandas-base-3/" target="_self">
Pandas: Pandas入门笔记(3)————电信客户流失数据集的分析
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