|What is it?||How does it work?||Features|
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Supported types of experiments include:
Qualimap examines sequencing alignment data in SAM/BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.
Starting from version 2.0 Qualimap provides multi-sample comparison of alignment and counts data.
|Latest package for GNU Linux, MacOS and MS Windows:
Source code (GPL v.2)
Latest development snapshots
Public code repository
CIPF BioInfo local Maven repository
QualiMap Online User Manual
Sample data and output can be found here
Picard: a Java API (SAM-JDK) for creating programs that read and write SAM files.
FastQC: a quality control tool for high throughput sequence data.
SAMTools: essential utilities for manipulating alignments in the SAM format.
NOISeq: quality control and differential gene expression analysis for RNA-seq data.
Repitools: quality assessment, visualization, summarization and statistical analysis of epigenomics experiments.
Software development links:
JProfiler: an award-winning all-in-one Java performance profiler.