Qualimap: evaluating next-generation sequencing alignment data

García-Alcalde, Fernando; Okonechnikov, Konstantin; Carbonell, José; Cruz, Luis Miguel González; Götz, Stefan; Tarazona, Sonia; Dopazo, Joaquı́n; Meyer, Thomas F.; Conesa, Ana

doi:10.1093/bioinformatics/bts503

Cited by 867 publications

(615 citation statements)

References 12 publications

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“…For each of the genomes, the complete set of raw reads was mapped to the CEGMA output files using the Burrows-Wheeler Aligner, BWA-MEM (v.0.7.8), with default settings (59). Coverage was calculated using QualiMap 2 (60). Under the assumption that the coverage estimated from the conserved CEGMA-identified regions is representative of genome-wide coverage, the number of base pairs used in the whole read set for each assembly was divided by the calculated coverage for that species, thus providing an estimate of the genome size for each species (Table 2).…”

Section: Methodsmentioning

confidence: 99%

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

Chang

Neuhof

Rubinstein

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

221

304

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The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell-cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.Myxozoa | Cnidaria | Polypodium | parasite | genome evolution

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Section: Methodsmentioning

confidence: 99%

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

Chang

Neuhof

Rubinstein

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

221

304

View full text Add to dashboard Cite

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“…A BurrowsWheeler aligner was used to align the sequencing reads onto the human reference genome (UCSC hg19). The aligned sequencing reads were evaluated using Qualimap (40), and the sequences were deposited in the Sequence Read Archive database (Project ID: PRJNA297066).…”

Section: Methodsmentioning

confidence: 99%

Whole-exome sequencing identifies recurrent AKT1 mutations in sclerosing hemangioma of lung

Jung

Kim

Lee

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Pulmonary sclerosing hemangioma (PSH) is a benign tumor with two cell populations (epithelial and stromal cells), for which genomic profiles remain unknown. We conducted exome sequencing of 44 PSHs and identified recurrent somatic mutations of AKT1 (43.2%) and β-catenin (4.5%). We used a second subset of 24 PSHs to confirm the high frequency of AKT1 mutations (overall 31/68, 45.6%; p.E17K, 33.8%) and recurrent β-catenin mutations (overall 3 of 68, 4.4%). Of the PSHs without AKT1 mutations, two exhibited AKT1 copy gain. AKT1 mutations existed in both epithelial and stromal cells. In two separate PSHs from one patient, we observed two different AKT1 mutations, indicating they were not disseminated but independent arising tumors. Because the AKT1 mutations were not found to cooccur with β-catenin mutations (or any other known driver alterations) in any of the PSHs studied, we speculate that this may be the singlemost common driver alteration to develop PSHs. Our study revealed genomic differences between PSHs and lung adenocarcinomas, including a high rate of AKT1 mutation in PSHs. These genomic features of PSH identified in the present study provide clues to understanding the biology of PSH and for differential genomic diagnosis of lung tumors.pulmonary sclerosing hemangioma | whole-exome sequencing | AKT1 mutation | copy number alteration

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“…Library preparation was carried out using 1.5 lg of total RNA for each. The RNA-Seq readings were obtained from a 2 9 100 bp paired-end Illumina HiSeq 2000 single lane run for each condition investigated, followed by a quality check using Qualimap version 2.2 [7] and removal of adaptor sequences. The readings retained were merged using FLASH 1.…”

Section: Methodsmentioning

confidence: 99%

The exceptionality of stress response in Magnaporthe oryzae: a set of “salt stress-induced” genes unique to the rice blast fungus

et al. 2017

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The ability of pathogens to signal perception and adaptation to environmental changes is an important prerequisite for successful colonization of the host organism. Filamentous phytopathogenic fungi, for example, have to cope with rapid changes in the environment during invasive growth in planta. Consequently, they have evolved a range of specific factors contributing to environmental adaptation facilitating host invasion. In addition to conserved pathways, including genes participating in stress response, unique/individual genes within the pathogens might represent determinants of pathogenicity. Therefore, identification of unique genes could provide a set of excellent candidates for novel and specific fungicide targets. One of the environmental changes during host invasion comprises the accumulation of osmolytes, which are present in varying concentrations inside the plant. Transcriptional profiling of the rice blast fungus Magnaporthe oryzae undergoing osmotic stress revealed interesting results. We identified a set of 239 genes which were regulated significantly by salt stress. Among these ''salt stressregulated'' genes, 176 (75%) of the upregulated and all of the downregulated genes were found to have no homologues in yeast when interrogation against the yeast protein database was performed. Functional annotation analysis by InterProScan and clustering of genes based on gene ontology (GO) enrichment analysis was conducted to annotate each of the ''salt stress-regulated'' genes and to identify functional categories of biological processes associated with environmental stress response. Finally, we present a set of ''salt stress-regulated'' genes suggested as unique in the rice blast fungus.

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Qualimap: evaluating next-generation sequencing alignment data

Abstract: Qualimap is freely available from http://www.qualimap.org.

Cited by 867 publications

References 12 publications

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

Whole-exome sequencing identifies recurrent AKT1 mutations in sclerosing hemangioma of lung

The exceptionality of stress response in Magnaporthe oryzae: a set of “salt stress-induced” genes unique to the rice blast fungus

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