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Options: BAM Unsorted, BAM SortedB圜oordinate, BAM Unsorted SortedB圜oordinate (to create both unsorted. Specifies the type of BAM file to create. 20 (2012): 2678-2679.īIO2009-10799 from the Spanish Ministry of Economy and Competitiveness and BIO2008-05266-E/- associated to the EU funded program ERA-NET PathoGenoMics. A survey of best practices for RNA- seq data analysis Genome Biology (2016) 4. "Qualimap: evaluating next-generation sequencing alignment data."īioinformatics 28, no. "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data."įernando García-Alcalde et al. Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde Qualimap is a joint project of Max Planck Institute For Infection Biology andĬentro de Investigación Príncipe Felipe (CIPF) Latest package for GNU Linux, MacOS and MS Windows: Multi-sample comparison of alignment and counts data.Analysis of the adequasy of the sequencing depth in RNA-seq experiments.Alignment Map (BAM) file format, sequencingexperiment, Sequencing Reads, N/A. Computation and analysis of read counts obtained from intersectition of read alignments with genomic features The following page lists genomic read analyses and data files generated by.Analysis of the reads mapped inside/outside of the regions provided in GFF format.Easy to interpret summary of the main properties of the alignment data.Fast analysis accross the reference of genome coverage and nucleotide distribution.Starting from version 2.0 Qualimap provides multi-sample comparison of alignment and counts 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. 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.