QualiMap statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool QualiMap

Tool usage distribution map

This map represents all the scientific publications referring to QualiMap per scientific context
info info

Associated diseases

This word cloud represents QualiMap usage per disease context

Popular tool citations

chevron_left Alignment evaluation Assembly evaluation chevron_right
Want to access the full stats & trends on this tool?


QualiMap specifications


Unique identifier OMICS_02133
Name QualiMap
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.1.2
Stability Stable
Maintained Yes




No version available



  • person_outline Fernando García-Alcalde

Publications for QualiMap

QualiMap citations


Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe

PLoS Pathog
PMCID: 5944922
PMID: 29746563
DOI: 10.1371/journal.ppat.1006997

[…] error rate (-n) of 0.2 to assure high specificity. The PCR duplicates were removed with MarkDuplicates from the Picard tools (https://broadinstitute.github.io/picard). The mapping was evaluated with QualiMap []. […]


Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529T, a Vinegar Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery Acetifiers

Genome Announc
PMCID: 5908927
PMID: 29674558
DOI: 10.1128/genomeA.00330-18
call_split See protocol

[…] were obtained. The SPAdes genome assembler version 3.11.0 () was used to perform a de novo genome assembly, which yielded 163 contigs (>500 bp) and 202-fold coverage. The assembly was validated with QualiMap version 2.1 ().The draft genome sequence consists of 3,629,663 bp, with an overall G+C content of 59.14%. The genome annotation was performed with Rapid Prokaryotic Genome Annotation (Prokka) […]


Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn’s disease

PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] ds. Reagent contamination was controlled by barcoding all DNA samples and primers. The quality of reads was assessed by the Phred quality score and the reads mapping fold coverage was determined with qualimap_v2.2.1. The raw reads were assembled as described previously. Contigs <1000 bp and with coverage <10× were removed. Gene annotation was performed by the Rapid Annotations software at Subsyste […]


In host microevolution of Aspergillus fumigatus: A phenotypic and genotypic analysis

Fungal Genet Biol
PMCID: 5883321
PMID: 29477713
DOI: 10.1016/j.fgb.2018.02.003
call_split See protocol

[…] axy version 0.32.3) (, ). Reads were mapped to the Af293 reference genome (release 31, EnsemblFungi) using the very sensitive local align preset mode in Bowtie2 (). Mapping quality was assessed using Qualimap (, ). Single nucleotide polymorphism (SNP) detection was conducted using FreeBayes (). VCFtools vcf-isec was used to assess patterns amongst SNPs and to filter SNPs with a minimum coverage of […]


Foreign peptide triggers boost in pneumococcal metabolism and growth

BMC Microbiol
PMCID: 5870813
PMID: 29580217
DOI: 10.1186/s12866-018-1167-y
call_split See protocol

[…] owtie2–2.2.8) []. Cufflinks (cufflinks-2.2.1) and Cuffdiff were used to count reads and calculate differential gene expression []. Quality control and coverage were examined using FastQC (0.11.5) and Qualimap 2.2.1 []. The sequencing and coverage was on average 3557 times the genome size (ranging between 543 and 5220). The mean length of sequenced fragments was 141 bp. Mapping to the reference gen […]


Early and late feathering in turkey and chicken: same gene but different mutations

PMCID: 5863816
PMID: 29566646
DOI: 10.1186/s12711-018-0380-3

[…] uencing data to the turkey reference genome (Melgal5) [], the Samtools dedup function to remove duplicate reads [], the GATK IndelRealigner to perform local realignments of reads around indels [] and Qualimap to obtain mapping statistics []. […]

Want to access the full list of citations?
QualiMap institution(s)
Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain; Department of Molecular Biology, Max-Planck Institute for Infection Biology, Berlin, Germany

QualiMap reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review QualiMap