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。

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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

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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

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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

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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

• FASTQC 0.11.9
• BWA-0.7.17(r1188)
• samtools 1.13
• htslib 1.13
• bcftools 1.3
• sambamba 0.8.0
• bedtools2 2.30.0
• GATK 4.2.1.0
• vcftools 0.1.16
• JAX-CNV 1.1.0
• Annovar (2019Oct24)
• AnnotSV v3.0.9
• IGV v2.10.2
• IGV for web app

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Resource

• Linux for Biologists - Part1
• An introduction to Linux for bioinformatics
• Broad Institute - genomics public data on Google cloud
• Broad Institute - bundle - Mutect2
• GATK tutorial data

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Reference

• Applied Computational Genomics Course at UU
• GATK Resource bundle