fastQC

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转载最新推荐文章于 2025-09-10 22:21:01 发布 · 157 阅读

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原文链接：http://www.cnblogs.com/bioSci/p/4957215.html

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FastQC是一款用于高通量测序原始数据质量控制的工具，它能够从BAM、SAM或FastQ文件中导入数据，并提供一系列模块化的分析来快速评估数据的质量问题。FastQC的主要功能包括提供数据概览、生成汇总图表以及导出HTML报告。

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/

转载于:https://www.cnblogs.com/bioSci/p/4957215.html