YXF-测序仪和质量控制

1. 目前常用的测序仪
   Illumina: high-throughput sequenching
   IonTorrent: clinical application
   PacBio Sequel: long read sequencing
   MinION: portable, miniaturized device, robust and reliable
   原理暂时没有搞明白
2. 质量控制步骤--Quality control of data
   质量控制：通过删去一些错误的数据来提高数据质量
   质量控制步骤：Keep reads with an average quality over a threshold
   Trim back the ends of reads until the measurements are reliable
   Remove known synthetic sequences
   质量控制工具：Trimomatic, cutadapt,bbduk
3. FastQC的结果解读--Visualizing data quality
   FastQC is FASTQ quality visualization tool
   length histogram: how many sequences of each length the data contains
   quality histogram: 横轴是质量分数，纵轴是质量读数
4. 使用multiQC聚合fastqc的输出结果
   multiQC: Generate outputs that summarze multiple individual results.
   安装：source activate bioinfo
   conda install multiqc -y
   使用：Get and unpack the data
   Run fastqc and make it keep the data directories
   Run multiqc on the resulting directories
   最后生成一个multiqc_report.html 的输出结果