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    • 免疫组学

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      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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      https://civicdb.org/pages/about

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      突变注释
      • anneng

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      444b9e0d-663a-40c9-b39a-8ca18960dd62-image.png

      https://www.frontiersin.org/articles/10.3389/fgene.2022.956781/full
      CCAS: One-stop and comprehensive annotation system for individual cancer genome at multi-omics level

    • A

      Spark在生物信息领域的应用
      • anneng

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      A

      NIH-Genomics-Workshop-11_4_2019.pdf

    • A

      R Packages
      • anneng

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      https://cran.r-project.org/doc/manuals/R-exts.html#Debugging-compiled-code
      R包可能包括C/C++代码 可以直接使用R -d gdb 进行调试

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      数据分析pipeline
      • anneng

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      A

      https://www.nextflow.io/docs/latest/kubernetes.html
      24a898cb-8cb4-43fb-9a23-fe8388c9b75a-image.png
      nextflow支持k8s

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      标准组织
      • anneng

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      https://biom-format.org/
      The Biological Observation Matrix (BIOM) format

    • Z

      使用 UNITE ITS 参考序列训练 QIIME2 分类器
      • zhangfanglin

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    • A

      比对过程涉及的参数
      • anneng

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      A

      https://gist.github.com/crazyhottommy/ed73c7e2daee8383dccb35f224f99714
      获取唯一比对的序列
      samtools view -h my.bam | awk '$17 ~ /XA:/' || $1 ~ /^@/' | samtools view -bS - > my_unique.bam

      https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment

    • A

      DNA marker
      • anneng

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      https://www.genecalculators.net/

    • A

      GATK
      • anneng

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      https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07013-y
      Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework

    • A

      Population_Genetics_in_R
      • anneng

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    • A

      Python Bioinformatics tutorials
      • anneng

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      A

      Tiago Antao - Bioinformatics with Python Cookbook-Packt Publishing (2018).pdf

    • A

      PowerMarker
      • anneng

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      https://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi

    • A

      组装 assembly
      • anneng

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      https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
      从这个文章看 quast可以使用参考基因组进行质控 busco可以使用同系物进行质控

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      illumina 测序介绍
      • anneng

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      ffd5c5e1-1a95-4466-ab25-0b07b7aec304-image.png
      https://www.ecseq.com/support/ngs/why-do-the-reads-all-have-the-same-length-when-sequencing-differently-sized-fragments
      什么是文库片段长度?

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      序列模拟 reads simulator
      • anneng

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      https://bitesizebio.com/30700/choose-appropriate-ngs-data-simulator/

      https://www.nature.com/articles/nrg.2016.57
      A comparison of tools for the simulation of genomic next-generation sequencing data

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      QC质控流程
      • anneng

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      gatk使用笔记
      • anneng

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      https://www.biostars.org/p/54673/
      GATK consensus

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      植物 DNA barcode
      • anneng

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      https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147692
      Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates
      7e009364-8680-4b90-9910-153f11dc6d8d-image.png

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      Molecular markers 分子标记
      • anneng

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      GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

    • A

      Joining Illumina paired-end reads for classifying phylogenetic marker sequences
      • anneng

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