a tool for bam file QC: Qualimap

http://qualimap.bioinfo.cipf.es/

Evaluating next generation
sequencing alignment data

What is it?	How does it work?	Features
Qualimap 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.	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.	Fast analysis accross the reference of genome coverage and nucleotide distribution; Easy to interpret summary of the main properties of the alignment data; Analysis of the reads mapped inside/outside of the regions provided in GFF format; Insert size mean and median value calculation and plotting statistical distribution; Analysis of the adequasy of the sequencing depth in RNA-seq experiments; Clustering of epigenomic profiles.
Download	Documentation	Example Datasets
Latest package for GNU Linux, MacOS and MS Windows: qualimap_v0.6.zip Source code (GPL v.2) qualimap_v0.6_src.zip Version history	QualiMap Online Help Qualimap user manual (pdf)	Sample data can be found here
Support	Please cite	Contact
Please join the QualiMap Mailing List: Your email:	Garcia-Alcalde et.al, (2012) Qualimap: evaluating next generation sequencing aligmnent data, Bioinformatics (accepted) doi: 10.1093/bioinformatics/bts503 Additional links: 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. Repitools: quality assessment, visualization, summarization and statistical analysis of epigenomics experiments.	Bioinformatics Department Centro de Investigación Príncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico) 46013 Valencia, Spain http://bioinfo.cipf.es Team: Fernando Garcia-Alcalde (garcia(a)mpiib-berlin.mpg.de) Konstantin Okonechnikov (okonechnikov(a)mpiib-berlin.mpg.de) Jose Carbonell (jcarbonell(a)cipf(dot)es) Sonia Tarazona (starazona(a)cipf(dot)es) Stefan Götz (sgoetz(a)cipf(dot)es) Luis Miguel Cruz (sm.cruz(a)juntadeandalucia(dot)es) Javier Santoyo (jsantoyo(a)cipf(dot)es) Joaquin Dopazo (jdopazo(a)cipf(dot)es) Ana Conesa (aconesa(a)cipf(dot)es)

QualiMap screenshots: