QualiMap pipeline

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

 (13)
2018
PMCID: 5764994
PMID: 29323241
DOI: 10.1038/s41598-017-19072-5

[…] pig genome (sscrofa10.2) and the annotation database ensembl genes 86 using the open-source software star 2.5.2a51. mapping quality evaluation and descriptive statistics were generated with qualimap v.2.252. the resulting bam files containing the aligned sequences were subsequently merged with samtools53. the total number of genome-mapped reads to gene was quantified using htseq. […]

2018
PMCID: 5786680
PMID: 29371354
DOI: 10.1128/genomeA.01517-17

[…] the spades genome assembler version 3.8.0 (7). the assembly resulted in 101 contigs (>500 bp), with an average coverage of 93×. the assembly was validated and the read coverage determined with qualimap version 2.1 (8)., the draft genome of b. mycoides gm5lp consisted of 6,016,834 bp, with an overall gc content of 35.08%. gene prediction and annotation were performed using prokka (rapid […]

2018
PMCID: 5794933
PMID: 29437086
DOI: 10.1128/genomeA.00011-18

[…] the spades genome assembler version 3.8.0 (8). the assembly resulted in 96 contigs (>500 bp) and an average coverage of 87-fold. the assembly was validated and the read coverage determined with qualimap version 2.1 (9)., the draft genome of gm6lp consists of 6,015,410 bp, with an overall gc content of 35.07%. gene prediction and annotation were performed using rapid prokaryotic genome […]

2018
PMCID: 5919401
PMID: 29698522
DOI: 10.1371/journal.pone.0196334

[…] using fastqc (v0.11.5; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). reads were aligned on the ucsc hg19 reference genome using bwa (v0.7.5) [11]. mapping quality was evaluated using qualimap (v2.2.1) [12]. duplicate read marking and all bam file manipulations were done using picardtools (v2.6.0; https://broadinstitute.github.io/picard/). reads from the na12882 platinum genome […]

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 (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%), […]

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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