QualiMap protocols

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QualiMap specifications

Information


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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Maintainer


  • person_outline Fernando García-Alcalde <>

Publications for QualiMap

QualiMap in pipelines

 (48)
2018
PMCID: 5764994
PMID: 29323241
DOI: 10.1038/s41598-017-19072-5

[…] reference pig genome (sscrofa10.2) and the annotation database ensembl genes 86 using the open-source software star 2.5.2a. mapping quality evaluation and descriptive statistics were generated with qualimap v.2.2. the resulting bam files containing the aligned sequences were subsequently merged with samtools. the total number of genome-mapped reads to gene was quantified using htseq. 0.6.1p2 […]

2018
PMCID: 5794457
PMID: 29435412
DOI: 10.1002/2211-5463.12360

[…] sequences and low‐quality sequences (reads presenting ambiguous bases denoted as ‘n’) were also trimmed from the raw data. the quality of analyzed data was checked using fastqc (v.0.11.5) and qualimap (v.2.2.1) software. the filtered data were then analyzed by clc genomics workbench v.10.0.1 (qiagen aarhus, denmark; https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/) […]

2018
PMCID: 5897801
PMID: 29650586
DOI: 10.1128/genomeA.00334-18

[…] reads. de novo genome sequence assembly was performed with spades version 3.11.1 (), which yielded 90 contigs (>500 b) with an average coverage of 175-fold. the results were validated with qualimap version 2.2.1 ()., the draft genome of c. vincentii consists of one chromosome (3.506 mb) exhibiting an overall g+c content of 30.7%. automatic gene prediction and identification of rrna […]

2018
PMCID: 5920165
PMID: 29700162
DOI: 10.1128/genomeA.00357-18

[…] genome assembly was performed with the spades genome assembler software version 3.10.0 (), yielding 63 contigs (>500 bp) and an average coverage of 103-fold. to validate the de novo assembly, qualimap version 2.1 was employed (). the draft genome was 2.629 mb, with a gc content of 53.52%. for gene prediction and annotation, the software tool prokka was employed (). gene prediction yielded […]

2018
PMCID: 5920174
PMID: 29700155
DOI: 10.1128/genomeA.00324-18

[…] 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 (). 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%), […]


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QualiMap in publications

 (123)
PMCID: 5920191
PMID: 29700154
DOI: 10.1128/genomeA.00323-18

[…] genome assembler software version 3.11.0 (). the assembly resulted in 69 contigs (>500 bp) and an average coverage of 96-fold. the assembly was validated and the read coverage determined with qualimap version 2.1 (). the resulting draft genome is 5.178 mbp in length, and the gc content is 35.17%. automatic annotation and identification of rrna and trna genes were performed using […]

PMCID: 5920165
PMID: 29700162
DOI: 10.1128/genomeA.00357-18

[…] genome assembly was performed with the spades genome assembler software version 3.10.0 (), yielding 63 contigs (>500 bp) and an average coverage of 103-fold. to validate the de novo assembly, qualimap version 2.1 was employed (). the draft genome was 2.629 mb, with a gc content of 53.52%. for gene prediction and annotation, the software tool prokka was employed (). gene prediction yielded […]

PMCID: 5912743
PMID: 29684056
DOI: 10.1371/journal.pone.0196290

[…] mapped on to the reference genome of b. breve (genbank accession ap012324) or b. longum (genbank accession nc_015067.1) using bowtie2 [] and the results were converted to bam format for viewing in qualimap v2.2.1 []. high quality reads were assembled with soapdenovo2 [] using the estimated average insert size from qualimap analysis., genomes sequenced in this study were annotated using […]

PMCID: 5908927
PMID: 29674558
DOI: 10.1128/genomeA.00330-18

[…] 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 […]

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

[…] 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 […]


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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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