PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment

Abstract

Pleurotus opuntiae is an important mushroom from xerophytic temperate regions of Mexico, as parasite or saprobe on Agave and Opuntia. Discussions on the taxonomic relationships of P. opuntiae with P. djamor, P. agaves, P. levis, and P. yuccae are presented, of which P. agaves is a synonym of P. opuntiae, and P. yuccae is a synonym of P. djamor. This latter and P. levis are close species of P. opuntiae. The traditional uses of P. opuntiae and P. djamor as food and remedy for several health problems, and also to get a traditional alcoholic drink from the Agave, are also considered. " 2012 Begell House, Inc.",,,,,,"10.1615/IntJMedMushr.v14.i1.70",,,"http://hdl.handle.net/20.500.12104/43669","http://www.scopus.com/inward/record.url?eid=2-s2.0-84859514210&partnerID=40&md5=b9497d2a5dd8e29b4ac6c6a96c0f16e9",,,,,,"1",,"International Journal of Medicinal Mushrooms",,"65

78",,"14",,"Scopus

WOS",,,,,,"Edible; Medicinal mushrooms; Parasites; Pleurotus opuntiae; Saprobes; Species of genus pleurotus",,,,,,"Pleurotus opuntiae (Durieu et Lév.) Sacc. (higher Basidiomycetes) and other species related to Agave and Opuntia plants in Mexico-Taxonomy, distribution, and applications",,"Article" "45424","123456789/35008",,"Ortiz-Villalobos, R.C., Médico ginecoobstetra, coordinador del servicio de Obstetricia, Hospital General de Occidente, Secretaría de Salud de Jalisco; Luna-Covarrubias, E.E., Médica ginecoobstetra adscrita al servicio de Obstetricia, Hospital General de Occidente de la Secretaría de Salud de Jalisco; Serrano-Enríquez, R.F., Médico ginecoobstetra, coordinador del servicio de Ginecología, Hospital General de Occidente de la Secretaría de Salud de Jalisco; Laureano-Eugenio, J., Maestro en Ciencias de la Salud Pública, Adscrito al Departamento de Investigación Estatal de la Secretaría de Salud de Jalisco; Mejía-Mendoza, M.L., Profesora en el Departamento de Salud Pública, Universidad de Guadalajara, Mexico; Rodríguez-Rodríguez, J.G., Especialista en nutrición clínica, Jefe del Departamento de Investigación Estatal, Secretaría de Salud de Jalisco",,"Ortiz-Villalobos, R.C.

Luna-Covarrubias, E.E.

Serrano-Enriquez, R.F.

Laureano-Eugenio, J.

Mejia-Mendoza, M.L.

Rodriguez-Rodriguez, J.G.",,"2013",,"Placental acretism is the abnormal adherence beyond the underlying of the uterine muscle. The penetration of the serous is known as placenta percreta. The following is a clinical study of a 28 year old woman, who had undergone 2 previous C-Sections, who had been admitted to the hospital previously with ultrasounds suggestive of placental acretism. The magnetic resonance show with severe infiltration of the myometrium in the anterior and lateral right, extending until the mesentery of the abdomen, top of the bladder and the proximal portion of the urethra as well as the soft tissue of the perinea. Cesarean section was performed at 35 weeks of gestation, once the complete protocol of the placenta previa, had been completed. The placentary tissue invaded the bladder, wide ligament along the entire right side and the posterior pelvis. A hysterectomy was performed in the fundic region, resulting in a live birth, and no complications for the patients. Later an obstetric hysterectomy was performed. It is important to note the exemplary work of the gynecologist, surgeon, urologist, anesthesiologist, neonatal specialist, hematologist and intensive care workers, working together for a common goal: avoiding the morbidity and mortality of the mother and child.",,,,,,,,,"http://hdl.handle.net/20.500.12104/43645","http://www.scopus.com/inward/record.url?eid=2-s2.0-84881622401&partnerID=40&md5=ad3aec6e4b24b133ba0d0ec141fd2b31",,,,,,"8",,"Ginecologia y Obstetricia de Mexico",,"487

493",,"81",,"Scopus",,,,,,"Abdominal wall; Bladder; Placenta percreta; Ureter",,,,,,"Placenta percreta with invasion of the bladder, ureter and abdominal wall. case report [Placenta percreta con invasión a la vejiga, el uréter y la pared abdominal. caso clúnico]",,"Article" "45413","123456789/35008",,"Martínez-Alcantara, A., Department of Computer Science, University of Houston, Houston, TX, United States; Ballesteros, E., Department of Computer Science, University of Houston, Houston, TX, United States, Department of Physics, Universidad de Guadalajara, Jalisco, Mexico; Feng, C., Department of Computer Science, University of Houston, Houston, TX, United States; Rojas, M., Department of Computer Science, University of Houston, Houston, TX, United States; Koshinsky, H., Eureka Genomics Corp., Houston, TX, United States; Fofanov, V.Y., Eureka Genomics Corp., Houston, TX, United States; Havlak, P., Department of Computer Science, University of Houston, Houston, TX, United States; Fofanov, Y., Department of Computer Science, University of Houston, Houston, TX, United States",,"Martinez-Alcantara, A.

Ballesteros, E.

Feng, C.

Rojas, M.

Koshinsky, H.

Fofanov, V.Y.

Havlak, P.

Fofanov, Y.",,"2009",,"PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and cycle-by-cycle graphical representation of clusters density, quality scores and nucleotide frequencies allow easy identification of various technical problems including defective tiles, mistakes in sample/library preparations and abnormalities in the frequencies of appearance of sequenced genomic reads. PIQA is written in the R statistical programming language and is compatible with bustard, fastq and scarf Illumina G1 Genome Analyzer data formats. " 2009 The Author(s).