病原微生物高通量测序数据分析笔记
关于笔记
- 关于示例
- Linux Shell
基因组数据处理
基因组数据比较
元基因组数据分析
- 16s rRNA Metagenomics
  - 文库制备注意事项
- Shotgun Metagenomics
  - ViroCap
  - Meta-BEETL
  - SUPRI
专题
常用软件的安装与设置
- Others
  - SRA_toolkit
  - edirect
- Trimming
- Assembly
  - SPAdes
  - MaSuRCA
  - A5_miseq
  - Velvet
- Mapping
  - samtools
  - bowtie2
  - bwa
- Visualization
  - circos
  - Artemis
  - BRIG
- Alignment
  - Blast 和 Blast+
  - mafft
- Phylogeny
  - RaxML
  - PhyML
- Anotation
  - Prokka
  - GeneMakerS
附录

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Alignment

序列比对

Blast
mafft

Local Alignment

Global Alignment

Whole Genome Alignment

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