Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.
Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22.
The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide sequence alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds of millions of reads. Often, the sequencing technology, protocol and/or the selected mapping algorithm introduce some unwanted biases in these data. The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses.
We have developed Qualimap, a Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides graphical and statistical analyses for the evaluation of data. Such quality-control data are vital for highlighting problems in the sequencing and/or mapping processes, which must be addressed prior to further analyses.
Qualimap is freely available from http://www.qualimap.org.
序列比对/映射 (SAM) 和二进制比对/映射 (BAM) 格式已成为下一代测序数据核苷酸序列比对的标准表示方法。SAM/BAM 文件通常包含数十到数亿个读取的信息。通常，测序技术、方案和/或所选的映射算法会在这些数据中引入一些不必要的偏差。系统地检测这些偏差是一项非常重要的任务，对于驱动适当的下游分析至关重要。
我们开发了 Qualimap，这是一个 Java 应用程序，通过考虑序列特征及其基因组特性，支持用户友好的映射数据质量控制。Qualimap 采用序列比对数据，并提供图形和统计分析，以评估数据。这些质量控制数据对于突出测序和/或映射过程中的问题至关重要，在进行进一步分析之前，必须解决这些问题。
Qualimap 可从 http://www.qualimap.org 免费获得。
