AfterQC: automatic filtering, trimming, error removing and quality control for fastq data.
AfterQC: automatic filtering, trimming, error removing and quality control for fastq data.
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AfterQC：fastq数据的自动过滤、修剪、错误消除和质量控制
DOI：
10.1186/s12859-017-1469-3
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发表时间：
2017-03-14
影响因子：
3
通讯作者：
Gu J
中科院分区：
文献类型：
--
作者：
Chen S;Huang T;Zhou Y;Han Y;Xu M;Gu J
背景一些应用，特别是那些对测序数据精度要求很高的临床应用，通常不得不面对不可避免的测序错误带来的麻烦。已经提出了几种工具来描述测序质量，但很少有工具能够量化或纠正测序错误。这一未得到满足的要求促使我们开发AfterQC，这是一种工具，具有分析测序错误并纠正大多数错误的功能，以及高度自动化的质量控制和数据过滤功能。与大多数工具不同，AfterQC针对配对末端测序数据分析配对序列的重叠。基于重叠分析，AfterQC可以检测和切割接头，并提供了一种新的功能来纠正重叠区域中的错误碱基。另一项新功能是检测和可视化测序气泡，这种气泡通常可以在流动细胞通道上找到，可能会引起测序错误。除了正常的每周期质量和碱基内容绘制外，AfterQC还提供Polyx(相同碱基X的长子序列)过滤、自动裁剪和基于K-mer的链偏差剖析等功能。结果对于每一个FASTQ文件，AfterQC过滤出错误的读取，检测并消除测序仪的气泡效应，修剪前后读数，检测测序错误并纠正部分错误，最终输出干净的数据并生成带有交互图形的HTML报告。在QC可在批处理模式下运行并支持多进程后，它可以与单个FASTQ文件、单个FASTQ文件对(用于配对末端排序)或用于自动处理所有包含的FASTQ文件的文件夹一起运行。在重叠分析的基础上，AfterQC可以估计排序错误率，并描绘误差变换分布。我们的错误剖析测试结果表明，错误分布与平台高度相关。结论AfterQC不仅仅是另一个新的质量控制(QC)工具，它能够自动执行质量控制、数据过滤、错误剖析和基础纠正。实验结果表明，AfterQC可以帮助消除对端测序数据的测序误差，提供更干净的输出，从而有助于减少假阳性变异，特别是对于低频率的体细胞突变。在提供丰富的可配置选项的同时，AfterQC可以自动检测和设置所有选项，大多数情况下不需要参数。
BackgroundSome applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling.ResultsFor each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer’s bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent.ConclusionMuch more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.