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



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  • person_outline Fernando García-Alcalde <>

QualiMap articles

QualiMap citations

PMCID: 5944922

[…] 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 [55]., after mapping and duplicate removal, the genome analysis toolkit (gatk) [56] was used to generate a mapping assembly for each sample that had at least 60% genome coverage […]

PMCID: 5920174

[…] of 73-fold for e. salina swb007 and 312 contigs (>500 bp) with an average coverage of 75-fold for e. salina swb005. the assemblies were validated and the read coverage was determined with qualimap version 2.1 (8). the resulting draft genomes are 10,602,813 bp (e. salina swb007) and 9,010,436 bp (e. salina swb005) in length, and the g+c contents are 68.1% and 69.5% (difference, 1.4%), […]

PMCID: 5870813

[…] [15]. cufflinks (cufflinks-2.2.1) and cuffdiff were used to count reads and calculate differential gene expression [16]. quality control and coverage were examined using fastqc (0.11.5) and qualimap 2.2.1 [17]. 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 […]

PMCID: 5552989

[…] spades genome assembler software version 3.8.0 (5) and resulted in 108 contigs (>500 bp), with an average coverage of 112-fold. the assembly was validated and the read coverage determined with qualimap version 2.1 (6). the draft genome of p. oleovorans dsm 1045 consisted of a single chromosome (4.86 mb) with an overall g+c content of 62.07%. automatic gene prediction and identification […]

PMCID: 5342587

[…] the alignment run with default parameters but allowing for a genome multihit search and transcriptome build and mapping. alignment quality metrics were collected using qualimap version 2.0.1 [55] (max planck institute for infection biology and bioinformatics department). quantification of feature alignments was performed using htseq-counts from htseq framework […]

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

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