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DIGI+ Talent 2023

DIGI+ Talent 跨域數位人才加速躍升計畫

Overview

本課程將以生物資訊的角度切入,對NGS(Illumina based)基因數據分析提供基本概念與實作分析進行全面介紹。主要目標是讓學員具有理論基礎及獨立的基因組分析操作能力,非常適合初學者。

課程中涵蓋關鍵概念和分析策略。 將探索由現代 DNA 定序技術帶來的一系列生物學問題,包括序列比對,遺傳變異鑑定,結構變異分析等。


Course lecture slide

  1. Course overview and Introduction to Linux
  2. Intruduction to NGS Technologies
  3. NGS Analysis Flow
  4. NGS Alignment
  5. NGS Variant Calling (Germline/Somatic)
  6. NGS SV/CNV Calling
  7. NGS Variant Annotation for Clinical

Hands-On

NCHC resource

  • 計畫代號:ACD112105

  • 計算資源:ngscourse

  • 軟體安裝路徑

    • /opt/ohpc/Taiwania3/pkg/biology
  • 使用方式:

    • 使用SLURM排程系統來送出工作

    • SLURM Job Script (CPU Queue)範例如下:

    #!/usr/bin/sh
    #SBATCH -A ACD111077                         # Account name/project number
    #SBATCH -J digiplus_talent                   # Job name
    #SBATCH -p ngs48G                            # Partition Name 等同PBS裡面的 -q Queue name
    #SBATCH -c 14                                # 使用的數 請參考Queue資源設定 
    #SBATCH --mem=46g                            # 使用的記憶體量 請參考Queue資源設定
    #SBATCH -o bwa_out.log                       # Path to the standard output file 
    #SBATCH -e bwa_err.log                       # Path to the standard error ouput file
    #SBATCH [email protected]  # email
    #SBATCH --mail-type=BEGIN,END                # 指定送出email時機 可為NONE, BEGIN, END, FAIL, REQUEUE, ALL
    
    echo 'Hello world!'  ##這邊寫入你要執行的指令

Reference Genome

  • Human
    • HG19

      /opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa

    • HG38

      /opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa

Annotation Reference Genome

  • Human

    • HG19

    /opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19

    • HG38

    /opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38


NGS Tools

/opt/ohpc/Taiwania3/pkg/biology/BWA/BWA_v0.7.17
/opt/ohpc/Taiwania3/pkg/biology/sambamba/sambamba_v0.8.1
/opt/ohpc/Taiwania3/pkg/biology/SAMTOOLS/SAMTOOLS_v1.13/bin
/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.3.0
/opt/ohpc/Taiwania3/pkg/biology/AnnotSV/AnnotSV_v3.0.9/bin
/opt/ohpc/Taiwania3/pkg/biology/ANNOVAR/annovar_20210819
/opt/ohpc/Taiwania3/pkg/biology/FastQC/FastQC_v0.11.9
/opt/ohpc/Taiwania3/pkg/biology/IGV/IGV_v2.10.3
/opt/ohpc/Taiwania3/pkg/biology/VCFtools/vcftools_v0.1.16/bin

Resource


Reference

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2023 DIGI+ Talent跨域數位人才加速躍升計畫

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