fastQC

Fastqc用途

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

主要功能

The main functions of FastQC are

• Import of data from BAM, SAM or FastQ files (any variant)
• Providing a quick overview to tell you in which areas there may be problems
• Summary graphs and tables to quickly assess your data
• Export of results to an HTML based permanent report
• Offline operation to allow automated generation of reports without running the interactive application

下载地址

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

运行需求

A suitable Java Runtime Environment,

$ Java -version #查找版本是否符合要求，>=1.6 OK

The Picard BAM/SAM Libraries (included in download)

 安装

无须安装，下载解压缩后直接运行

详细说明

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt

Windows

Windows: Simply double click on the run_fastqc bat file.  If you want to make a pretty 
shortcut then we've included an icon file in the top level directory so you don't have
to use the generic bat file icon.

Linux

Linux:  We have included a wrapper script, called 'fastqc' which is the easiest way to 
start the program.  The wrapper is in the top level of the FastQC installation.  You 
may need to make this file executable:chmod 755 fastqc..but once you have done that you can run it directly./fastqc..or place a link in /usr/local/bin to be able to run the program from any location:sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc

命令行操作

fastqc --help

e.g. 

fastqc -i input.fastq -o Out_dir

结果输出

Summary

• Basic Statistics
• Per base sequence quality
• Per tile sequence quality
• Per sequence quality scores
• Per base sequence content
• Per sequence GC content
• Per base N content
• Sequence Length Distribution
• Sequence Duplication Levels
• Overrepresented sequences
• Adapter Content
• Kmer Content

 点击查看每个部分，详细解读

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/