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site_name: 杭州市疾控中心测序实验室
site_description: '杭州市疾控中心测序实验室'
site_author: 'indexofire'
site_url: 'https://indexofire.github.io/pathongs/'
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copyright: 'Copyright © 2016 - 2021 HZCDC@Lab'
repo_url: https://github.com/indexofire/pathongs/
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palette:
primary: 'blue'
extra_css:
- assets/stylesheets/extra.css
nav:
- '首页': index.md
- '数据分析笔记':
- '第零章 开始之前': book/main.md
- '第一章 常用工具':
- '01. 基因组公共数据库': book/C01_Common-Utility/01_database.md
- '02. 下载基因组数据': book/C01_Common-Utility/02_get-data.md
- '03. Entrez 工具': book/C01_Common-Utility/03_entrez.md
- '04. EMBOSS 工具集': book/C01_Common-Utility/04_emboss.md
- '05. Blast 比对': book/C01_Common-Utility/05_blast.md
- '06. FastQC': book/C01_Common-Utility/06_fastqc.md
- '07. Multiqc': book/C01_Common-Utility/07_multiqc.md
- '08. SeqKit 工具': book/C01_Common-Utility/08_seqkit.md
- '09. Kmer 工具': book/C01_Common-Utility/09_kmer.md
- '第二章 组装与比对':
- '01. 基本比对流程': book/C02_Raw-Data-to-Genome/01_bwa-samtools-pipeline.md
- '02. Quast 验证': book/C02_Raw-Data-to-Genome/02_quast.md
- '03. 细菌基因组组装': book/C02_Raw-Data-to-Genome/03_bacteria-assembly.md
- '04. 病毒基因组组装': book/C02_Raw-Data-to-Genome/04_virus-assembly.md
- '05. GATK3': book/C02_Raw-Data-to-Genome/05_gatk3.md
- '06. GATK4': book/C02_Raw-Data-to-Genome/06_gatk4.md
#- '10. snap': C04_Pathogen-Genome-Assembly/10_snap.md
- '11. 长序列比对': book/C02_Raw-Data-to-Genome/11_long-noisy-reads-assembly.md
- '12. 二代三代混合组装': book/C02_Raw-Data-to-Genome/12_hybrid-assembly.md
- '14. bwa 长序列比对': book/C02_Raw-Data-to-Genome/14_bwa-long-sequence-mapping.md
#- '15. whatshap': C04_Pathogen-Genome-Assembly/15_whatshap.md
- '第三章 基因组注释':
- '01. Prokka 快速注释': book/C03_Genome-Annotation/01_prokka.md
- '02. 在线注释工具 rast': book/C03_Genome-Annotation/02_rast.md
- '03. 注释工具 PGAAP': book/C03_Genome-Annotation/03_pgaap.md
- '04. SNP注释工具 snpEFF': book/C03_Genome-Annotation/04_snpeff.md
- '05. COG注释': book/C03_Genome-Annotation/05_cog.md
- '第四章 基因组比较':
- '01. mummer': book/C06_Genome-Compare/01_mummer.md
- '02. nucdiff': book/C06_Genome-Compare/02_nucdiff.md
- '03. mauve': book/C06_Genome-Compare/03_mauve.md
- '04. sibelia': book/C06_Genome-Compare/04_sibelia.md
- '05. ani': book/C06_Genome-Compare/05_ani.md
- '10. bigsi': book/C06_Genome-Compare/10_bigsi.md
- '第五章 泛基因组分析':
- '01. Pangenome 概述': book/C07_PanGenome-and-CoreGenome/01_pangenome.md
- '02. Get_Homologues 分析': book/C07_PanGenome-and-CoreGenome/02_get_homologues.md
- '03. BPGA 分析': book/C07_PanGenome-and-CoreGenome/03_bpga.md
- '04. Roary 分析': book/C07_PanGenome-and-CoreGenome/04_roary.md
- '05. panseq 分析': book/C07_PanGenome-and-CoreGenome/05_panseq.md
- '07. OrthMCL 分析': book/C07_PanGenome-and-CoreGenome/07_orthmcl.md
- '08. ITEP 分析': book/C07_PanGenome-and-CoreGenome/08_itep.md
- '第六章 基因组可视化':
- '01. igv 查看比对结果': book/C08_Genome-Visualization/01_igv.md
- '02. BRIG 分析工具': book/C08_Genome-Visualization/02_brig.md
- '03. circos 工具使用': book/C08_Genome-Visualization/03_circos.md
- '第七章 综合分析平台':
- '01. 基于 docker 镜像': book/C09_Analysis-Platform/01_docker.md
- '02. Galaxy 平台': book/C09_Analysis-Platform/02_galaxy.md
- '03. Amazon EC2 云平台': book/C09_Analysis-Platform/03_amazon.md
- '04. 其他平台': book/C09_Analysis-Platform/04_others.md
- '05. anvio': book/C16_Standalone-Platform/01_anvio.md
- '02. galaxy': book/C16_Standalone-Platform/02_galaxy.md
- '第八章 重组与种群分析':
- '01. 病毒重组': book/C10_Recombination-and-Population-Structure/01_virus-recombination.md
- '02. Gubbins 分析': book/C10_Recombination-and-Population-Structure/02_gubbins.md
- '03. BAPS': book/C10_Recombination-and-Population-Structure/03_baps.md
- '第九章 细菌扫描工具':
- '01. SRST2 短序列扫描工具': book/C11_Insilico-Scanning/01_srst2.md
- '02. MLST 扫描工具': book/C11_Insilico-Scanning/02_mlst.md
- '03. Ariba 耐药基因': book/C11_Insilico-Scanning/03_ariba.md
- '04. Abricate 多功能扫描工具': book/C11_Insilico-Scanning/04_abricate.md
- '第十章 宏基因组分析':
- '01. kraken': book/C12_Metagenomics-Analysis/01_kraken.md
- '02. centrifuge': book/C12_Metagenomics-Analysis/02_centrifuge.md
- '03. bracken': book/C12_Metagenomics-Analysis/03_bracken.md
- '04. sourmash': book/C12_Metagenomics-Analysis/04_sourmash.md
- '05. clark': book/C12_Metagenomics-Analysis/05_clark.md
- '06. krona': book/C12_Metagenomics-Analysis/06_krona.md
- '07. pavian': book/C12_Metagenomics-Analysis/07_pavian.md
- '08. supri': book/C12_Metagenomics-Analysis/08_supri.md
- '09. shotgun 分析': book/C12_Metagenomics-Analysis/09_shotgun.md
- '10. 16S 种群分析': book/C12_Metagenomics-Analysis/10_16s.md
- '11. KmerFinder': book/C12_Metagenomics-Analysis/11_kmerfinder.md
- '12. Meta-BEETL': book/C12_Metagenomics-Analysis/12_meta-beetl.md
- '第十一章 单分子测序':
- '01. nanopore': book/C13_Single-Molecular-Sequencing/01_nanopore.md
- '02. pacbio': book/C13_Single-Molecular-Sequencing/02_pacbio.md
- '03. canu': book/C13_Single-Molecular-Sequencing/03_canu.md
- '04. trimming': book/C13_Single-Molecular-Sequencing/04_seqs-polish.md
- '06. hybrid': book/C13_Single-Molecular-Sequencing/06_hybrid-assembling.md
- '第十二章 多重序列比对':
- '01. 多重序列比对': book/C14_Multiple-Sequence-Alignment/01_msa.md
- '第十三章 进化树构建分析':
- '00. 构建进化书': book/C15_Phylogeny-Analysis/00_all-about-phylogeny.md
- '01. RAxML': book/C15_Phylogeny-Analysis/02_raxml.md
- '02. figtree': book/C15_Phylogeny-Analysis/01_figtree.md
- '03. ggtree': book/C15_Phylogeny-Analysis/02_ggtree.md
- '第十七章 分子地理流行病学':
- '04. CartoDB': book/C17_Pathogen-Geospatial-Analysis/04_cartodb.md
- '05. leaflet': book/C17_Pathogen-Geospatial-Analysis/05_leaflet.md
- '第十八章 分析实践':
- '01. 细菌SNP溯源分析一': book/C18_Analysis-Examples/01_trace-Pae-from-different-source-by-SNP.md
- '02. 细菌比较基因组学研究': book/C18_Analysis-Examples/02_comparative-analysis-Ban-genomes.md
- '第十九章 工具流工具':
- '05. workflow工具软件': book/C19_Pipelines-and-Workflows/05_workflow-software.md
- '第二十章 其他':
- '02. GI转Accession': book/C20_Others/02_gi-to-accession.md
- '专项教程':
- '命令行工具下载基因组数据':
- '01. 简介': tutorial/CML-download/01_start.md
- '02. 下载Assembly': tutorial/CML-download/02_assembly.md
- '新冠病毒分析平台':
- '01. nextclade': tutorial/nCov/01_nextclade.md
- '02. nextstrain': tutorial/nCov/02_nextstrain.md
- 'Linux入门':
- '01. Linux 安装示例': tutorial/Linux/01_linux-installation.md
- '02. Linux 基本命令': tutorial/Linux/02_basic-cml.md
- '03. Linux 软件管理': tutorial/Linux/03_linux-software.md
- '04. awk 列处理工具': tutorial/Linux/04_awk.md
- '05. sed 行处理工具': tutorial/Linux/05_sed.md
- '06. 其他命令行工具': tutorial/Linux/06_tools.md
- '07. vim': tutorial/Linux/07_vim.md
- '常用编程语言':
- '01. Shell 脚本': tutorial/Programming/01_shell.md
- '02. Perl 编程': tutorial/Programming/02_perl.md
- '03. Python 编程': tutorial/Programming/03_python.md
- '04. Biopython 编程': tutorial/Programming/04_biopython.md
- '05. R 编程': tutorial/Programming/05_r.md
- '数据文件格式':
- '01. fasta': tutorial/Format/01_fasta.md
- '02. embl': tutorial/Format/02_embl.md
- '03. fastq': tutorial/Format/05_fastq.md
- '04. gcg': tutorial/Format/04_gcg.md
- '05. sam': tutorial/Format/05_sam.md
- '06. bam': tutorial/Format/06_bam.md
- '07. bed': tutorial/Format/07_bed.md
- '08. vcf': tutorial/Format/08_vcf.md
- '09. gff': tutorial/Format/09_gff.md
- '10. cram': tutorial/Format/10_cram.md
- '实验手册':
- '': protocol.md
- 'ArticNetwork Covid-19测序': protocol/artic-network-covid19.md
- '关于我们':
- '': about.md
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