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    • 免疫组学

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      A

      https://www.sc-best-practices.org/air_repertoire/ir_profiling.html
      56a55e24-8f0e-4b43-a73b-0ee7beaf8d4e-image.png

      VDJ过程
      adc29db5-511a-48a1-bd0f-e9269ac0a751-image.png

    • 细胞与基因疗法 cell and gene therapy

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      A

      Definition of Gene Therapy in the EU
      In the EU, the definition of a Gene Therapy Medicinal Product (GTMP) is provided
      in Directive 2009/120/EC amending Directive 2001/83/EC, part IV of Annex I.
      A GTMP means a biological medicinal product that has the following
      characteristics:
      (a) it contains an active substance that contains or consists of a recombinant
      nucleic acid used in or administered to human beings with a view to
      regulating, repairing, replacing, adding or deleting a genetic sequence;
      (b) its therapeutic, prophylactic or diagnostic effect relates directly to the
      recombinant nucleic acid sequence it contains, or to the product of the
      genetic expression of this sequence.
      GTMPs do not include vaccines against infectious diseases.
      Hazel Aranha, Humberto Vega-Mercado - Handbook of Cell and Gene Therapy_ From Proof-of-Concept through Manufacturing to Commercialization-CRC Press (2023).pdf

    • 代谢组学

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      A

      核磁在代谢组学中的应用

      1.核磁共振技术原理
      https://www.youtube.com/watch?v=pUWcXvw1Rsg
      https://www.bilibili.com/video/BV1CU4y1E7xL/?spm_id_from=333.788.recommend_more_video.-1(有中文翻译 比较好)

    • 司法

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      A

      https://bitbucket.org/rirgabiss/mhinngs/src/master/
      MHinNGS is a tool for analysis of microhaplotypes (MHs) in singleend sequencing data obtained through a massive parallel sequencing plattform (MPS). The tool identifies the reads with the MHs and calls the genotypes of the MHs according to the criteria and positions specified in the configuration file. It also searches for additional variants in the region defined by the start and the stop positions specified in the configuration file.
      这个软件的输入是参考序列和原始单端测序的fastq 包括了比对过程 依赖的第三方软件包括
      python 3.6 including pip
      samtools version 1.9
      hisat2 version 2.1.0
      stringtie version 2.0.3
      agrep T.R.E. version 0.8.0
      不支持双端序列

    • 表观遗传学

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      A

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828144/
      Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
      3d1f0fc6-d2ed-4539-9cde-0c03bde51949-image.png

    • 合成生物学

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      A

      https://github.com/mesoscope

    • 植物基因组学

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      M

      参考

      https://gatk.broadinstitute.org/hc/en-us/articles/360035531572-Evaluating-the-quality-of-a-germline-short-variant-callset

    • 蛋白组学

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      A

      https://www.sinobiological.com/resource/protein-review/fc-fusion-proteins
      46c1ca94-e2a9-44bd-b53e-593a82afcd3c-image.png

    • 临床生物信息

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      A

      1689181129856.gif

    • 肿瘤NGS数据分析

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      A

      https://civicdb.org/pages/about

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      烟草的基本信息
      • anneng

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    • A

      通过Hbase构建多组学融合数据库
      • anneng

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      A

      Introduction to Apache HBase(part 2) _ by Igor Skokov _ Medium.pdf
      用hbase存储目录结构

    • A

      genbank 和 refseq的对比
      • anneng

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    • A

      blast NT NR库readme介绍
      • anneng

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    • A

      序列注释分析一例
      • anneng

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    • A

      megan 相关材料
      • anneng

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      A

      直接在服务器上安装有问题 需要图形界面 我们把megan的tools 拷贝到服务器上即可 使用其中的 blast2lca 模块
      Unpacking JRE ...
      Starting Installer ...
      An error occurred:
      java.lang.NoClassDefFoundError: Could not initialize class java.awt.GraphicsEnvironment$LocalGE
      Error log: /tmp/install4jError16912109702133057733.log
      java.lang.NoClassDefFoundError: Could not initialize class java.awt.GraphicsEnvironment$LocalGE
      at java.desktop/java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:106)
      at java.desktop/sun.awt.X11.XToolkit.<clinit>(XToolkit.java:232)
      at java.desktop/sun.awt.PlatformGraphicsInfo.createToolkit(PlatformGraphicsInfo.java:40)
      at java.desktop/java.awt.Toolkit.getDefaultToolkit(Toolkit.java:592)
      at java.desktop/javax.swing.ImageIcon.<init>(ImageIcon.java:198)
      at java.desktop/javax.swing.ImageIcon.<init>(ImageIcon.java:217)
      at com.install4j.runtime.installer.frontend.GUIHelper.loadIcon(GUIHelper.java:193)
      at com.install4j.runtime.installer.frontend.GUIHelper.<clinit>(GUIHelper.java:52)
      at com.install4j.runtime.installer.frontend.headless.AbstractHeadlessScreenExecutor.init(AbstractHeadlessScreenExecutor.java:73)
      at com.install4j.runtime.installer.frontend.headless.ConsoleScreenExecutor.<init>(ConsoleScreenExecutor.java:24)
      at com.install4j.runtime.installer.frontend.headless.InstallerConsoleScreenExecutor.<init>(InstallerConsoleScreenExecutor.java:6)
      at com.install4j.runtime.installer.Installer.getScreenExecutor(Installer.java:87)
      at com.install4j.runtime.installer.Installer.runInProcess(Installer.java:56)
      at com.install4j.runtime.installer.Installer.main(Installer.java:45)
      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.base/java.lang.reflect.Method.invoke(Method.java:564)
      at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)
      at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66)
      at install4j.Installer959700663.main(Unknown Source)

    • A

      宏基因软件进行基线评估Community-driven challenges such as Critical Assessment of Metagenome Interpretation (CAMI)
      • anneng

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    • A

      megablast 和 blastn的差异
      • anneng

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    • A

      blast c++ toolkit 源码分析和使用
      • anneng

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      A

      toolkit第一次编译的时候就要选择debug或者release 一旦编译一个 切换另一个就会失败 我们先使用debug进行调试

    • A

      如何选择宏基因物种分类工具 Kraken, KrakenUniq, Kraken 2, and Centrifuge
      • anneng

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      A

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7257156/#CR22
      短读长和长读长对工具的影响

    • A

      口蹄疫病毒分型
      • anneng

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    • A

      按照物种进行blast过滤
      • anneng

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    • A

      基因组注释工具 SnpEff
      • anneng

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      SnpEff需要一个数据库来进行注释 已经支持的物种可以通过下面的命令查询:
      $ java -jar snpEff.jar databases | less
      下载数据库
      $ java -jar snpEff.jar download -v GRCh37.75

      如果对应物种没有数据库 可以自己做数据库
      https://pcingola.github.io/SnpEff/se_buildingdb/

    • A

      序列比对工具 对比分析
      • anneng

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      A

      https://en.wikipedia.org/wiki/List_of_sequence_alignment_software

    • A

      cactus 分布式加速方案
      • anneng

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      上面的图不正确 修正如下:
      f4478bdd-1886-4e11-a4b7-8e448bc00056-image.png

    • A

      cactus 多基因组比对技术分析
      • anneng

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    • A

      Google genomic-data-processing-reference-architecture
      • anneng

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    • A

      几种突变分析流程的对比
      • anneng

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    • A

      比对软件
      • anneng

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    • A

      比对软件中的 soft clips 和 hard clips 概念
      • anneng

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      A

      http://www.aigenetic.com/index.php/2018/03/19/soft-clip-与-hard-clip的含义描述/

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