QualiMap and a later version, Qualimap 2, is a tool for quality control of sequence alignments and genomic features. The QualiMap can use whole-genome genome and exome sequencing, RNA-seq, and ChIP-seq data. It also has functions for comparison of multiple samples and clustering of epigenomic profiles.
Data quality management
Garcia-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Gotz S, Tarazona S, Dopazo J, Meyer TF, Conesa A "Qualimap: evaluating next-generation sequencing alignment data." Bioinformatics. 2012 Oct 15;28(20):2678-9. Epub 2012 Aug 22. https://doi.org/10.1093/bioinformatics/bts503
PMID: 22914218
Okonechnikov K, Conesa A, García-Alcalde F "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data" Okonechnikov K1, Conesa A2, García-Alcalde F1. https://doi.org/10.1093/bioinformatics/btv566
PMID: 26428292
PMCID: PMC4708105
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