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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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      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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      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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      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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      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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      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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      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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      1689181129856.gif

    • 肿瘤NGS数据分析

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      A

      https://civicdb.org/pages/about

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      突变分析
      • anneng

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      https://merenlab.org/2012/05/11/oligotyping-pipeline-explained/
      b21e9632-ac1a-4c95-9f77-9aa9af85dc4b-image.png

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      Faster NGS Duplicate Marking
      • anneng

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      A

      https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1097-3#:~:text=PCR duplicates are sequence reads,duplicates appear proportionately more often
      这个文章说去重对后面的variant call 结果影响不大 但是这样能明显减少分析的数据量

    • A

      Dnanexus 帮助手册
      • anneng

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    • A

      DNA fingerprinting DNA指纹技术
      • anneng

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

    • A

      诺禾mNGS培训
      • anneng

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      mNGS采用的SE50 单端50bp的测序

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      新冠病毒数据分析
      • anneng

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      https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html
      3d45b431-f0f2-4fb8-8097-95ef568404a1-image.png

      b3923b0d-86a8-4cf0-a330-7faf0d318bfb-image.png

      8e618714-840f-4f27-985a-50420fdd0571-image.png

    • A

      gdc 一些数据分析资料
      • anneng

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    • A

      遗传多样性的指标
      • anneng

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      遗传多样性里面有一个很重要的概念 叫作haplotypes reconstruction 单倍型重构 在一个个体中 因为病毒的变异 可能会存在不同的 quasispecies 这些亚种如何用单倍型进行区分 对后续的治疗很有影响

      https://sci-hub.st/10.1093/bib/bbs081
      9f8b750e-0f25-4c5a-bdc3-f83966ea488d-image.png
      图中 淡蓝色和深色是两个不同的单倍型 不同reads 情况就比较复杂

    • A

      物种注释
      • anneng

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      A

      https://academic.oup.com/bib/article/19/3/495/2733162
      Comparing genome versus proteome-based identification of clinical bacterial isolates
      55e6d3da-3479-42f9-958d-002a12de02df-image.png

    • A

      食物欺诈 物种鉴定
      • anneng

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      https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0706-9
      Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing
      27488414-4a24-478c-b936-670fc2b5cbb0-image.png

    • A

      使用blast+megan 来分析物种
      • anneng

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      I

      准备工作 制作序列id和taxid的映射文件

      下载地址:
      https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/

      prot.accession2taxid.gz nucl_gb.accession2taxid.gz
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      Genbank GI vs accession id
      • anneng

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    • A

      Terra 对cromwell的架构解释
      • anneng

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    • A

      生信培训材料集
      • anneng

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    • A

      nextstrain调试记录
      • anneng

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      https://terra.bio/workflow-updates-to-the-covid-19-workspace-better-viral-assembly-and-phylogenetics-with-nextstrain/

      terra对nextstrain的支持

    • A

      美国CDC的一些流程
      • anneng

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    • A

      序列的可视化工具
      • anneng

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      https://github.com/a-slide/pycoQC
      pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
      0a859543-103d-449b-8a4f-595f7c03c2f2-image.png

    • A

      blast max_target_seqs max_hsps
      • anneng

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      /home/bioinfo/test_blast

      相关细节 在大服务器上 构建了一个测试 可以跑跑看看
      blastn -task blastn -query test.fasta -db db/db.fasta -dust no -max_hsps 1 -max_target_seqs 2 -qcov_hsp_perc 99

    • A

      使用Diamond basta进行物种分类
      • anneng

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      https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.59
      这个文章写的很好 推荐了 Diamond+megan LCA 里面也提到了为什么要对比蛋白库 (但是感觉有点牵强)主要的论点是核酸库毕竟已知的物种很少

    • A

      Calling variants in non-diploid systems
      • anneng

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