MASV, a misassembly detection and variant calling pipeline for long reads data

Trabajo fin de máster en Bioinformática y Biología ComputacionalIn de novo genome assembly each genome sequenced and assembled presents its own chal- lenges such as sample quantity, DNA integrity, repetitiveness, heterozygosity... but above all, mis-assemblies are often the most difficult ones to tackle. Fortunately the longer read size pro- duced by third generation sequencing technologies allow a better characterization of complex regions, usually differentiated by its large number of repeats [1],[2]. This masters project aims to develop an automated pipeline for detecting large structural variants (SV) in de novo assemblies produced by long reads which may be indicative of errors in the assembly process. By mapping these reads to their assembly we might be able to pinpoint mis-assemblies or sequence blocks with a high discrepancy to the real genomic fragment from which the read derived. Methodology: In order to do so a Snakemake pipeline was developed. It incorporates the most widely used aligners Minimap2 [3] and Ngmlr [4] as well as two SV prediction software Sniffles[4] and Svim[5]. It also includes custom scripts to measure recall, precision, F1 and precision-recall trade-off for evaluation purposes as well as some custom scripts for VCF (variant call file) formatting and conversion. Experiments conducted: First the SV predicting power was benchmarked replicating an experiment in the Svim paper[5]: using NA12878 nanopore raw reads (obtained from the Nanopore WGS consortium [6]) mapped against the hg19 human genome reference with 2676 high-confidence deletions and 68 high-confidence insertions as the high confidence SV dataset (validated in a previous study using PacBio and Moleculo reads [7]). After successfully repli- cating the experiment and setting the default parameters, the pipeline functionality was tested with respect to mis-assembly detection. This experiment involved simulating long reads from a reference genome into which we introduced Svs at known positions. The simulated reads would then be mapped to the unaltered reference in order to detect the rearrangements (i.e. “mis-assemblies”). In other words, the idea was for the unaltered hg19 reference to resemble a de novo assembly mis-assembled with respect to the reads (rearranged-based simulated reads), provided the reads are the "ground truth", and with the knowledge beforehand of where the real SV were located. The hg19 reference genome (in this case chromosomes 21 and 22 to avoid larger computation times in a more controlled environment) were rearranged introduc- ing simulated homozygous SVs. 200 deletions, 100 inversions, 200 tandem duplications and 100 insertions (cut & paste more akin to conservative transposition) were introduced using the R package RSVsim[8], providing us a high confidence “truth” SV dataset. The SimLoRD[9] python package was required to simulate PacBio reads (x53 coverage) based on the rearranged hg19 reference. Thus two conditions were proposed: rearranged-based reads mapped against the hg19 reference to test prediction in homozygosity; and a merge of simulated reads based on the rearranged reference (x26 coverage) and normal reference simulated reads (x26 coverage) for a total of x52 coverage heterozygous reads against the normal reference. Discussion: The results obtained are quite promising. With the caveat that only simulated data was used instead of an actual assembly, the results seem to indicate that long read SV detection methods can be used as a tool for mis-assembly detection. Though it is not imple- mented, it would have been interesting to merge the calls from both SV predictors, generating high confidence consensus calls to reduce the impact of spurious calls on complex genome assemblies, such as the ones from the plant kingdom[10]. Future work would focus development on an algorithm or reducing the number of mis-assemblies in draft genomes by rearranging the target assembly according to the calls made by the MASV pipeline

Lineamientos para un plan de gestión ambiental Vereda Agualinda, Apía Risaralda 2022

Partiendo de la metodología de Planeación Prospectiva Estratégica propuesta por la escuela francesa de Michel Godet se llevó a cabo un trabajo investigativo aplicado en la vereda Agualinda del municipio de Apía, Risaralda. Con el fin de comprender la Problemática Ambiental actual y tendencial de la vereda. Los procesos históricos que la han generado y por último dar lineamientos de gestión para construir el escenario apuesta en un horizonte de tiempo de 7 años. El trabajo de investigación se realizó durante 16 semanas y conto con la participación de diferentes actores académicos, sector privado, institucional y comunitari

Diseño e implementación de un laboratorio de energía fotovoltaica para ITCA-FEPADE Centro Regional San Miguel

El presente documento contiene información concerniente al proyecto de investigación realizado por docentes en colaboración con los estudiantes de la carrera de Técnico en Ingeniería Eléctrica del Centro Regional de San Miguel, denominado “Diseño e implementación de un laboratorio de energía fotovoltaica para ITCA-FEPADE Centro Regional San Miguel”. El objetivo principal era diseñar y construir un laboratorio para que los estudiantes y docentes puedan desarrollar las prácticas de la asignatura “energías renovables”. En este documento se encuentra contenida la siguiente temática: El planteamiento del problema de la investigación, en el cual se define de forma detallada la situación o problema a resolver con la construcción del laboratorio; los antecedentes de la institución que forman parte de la investigación preliminar y documentación necesaria para la realización del proyecto; la justificación del problema que responde a las preguntas del porqué de la investigación, quiénes son los beneficiarios directos e indirectos con este tipo de investigación. Se plantean también las hipótesis, que constituye uno de los ejes principales de toda investigación. Está plasmada en ella la pregunta a la cual se le dará respuesta con el desarrollo del proyecto. En el marco teórico está plasmada la teoría base y que fundamenta toda investigación, la cual se ha tomado como referencia para enriquecer y realzar el proyecto. La metodología constituye el mapa a seguir, los lineamientos y procedimientos necesarios para alcanzar los resultados deseados con el proyecto. Se presenta además la conclusión y recomendación, las cuales de forma descrita nos dan la pauta sobre aquellos conocimientos a los cuales se llegaron y así mismo las respuestas a cómo debería dársele seguimiento y explotación de las energías renovables

Hey children! Do you feel listened by your politicians? Evaluating a participative democratic programme

The objective of this study was to evaluate a participative democracy programme called Ágora infantil, carried out with students between the ages of 10 and 12. As in participatory budgets, the process is based on the research-action model (Lewin, 1946) and consists of the city council opening up decision-making on a part of the municipal budget or a concrete policy to the children of the municipality. This process of diagnosis, prioritization and decision-making was completed over the course of 5 to 7 sessions during school hours and implemented by the Coglobal association. Once the participants make a decision, the city council carries out the project selected in the municipality (the decision made is binding). The main goal of Ágora Infantil is to generate psychological empowerment and wellbeing amongst its participants, and to measure the effects of this programme on children’s psychological empowerment. To this end, we used Zimmerman´s model (Zimmerman, 1995; Zimmerman, 2000). The operationalization of the strengthening was based on: 1) knowledge of local politics (as a component of the interactional dimension of psychological empowerment) and 2) the self-perception of being able to influence the future of the municipality (component of the intrapersonal dimension of psychological empowerment). In addition, wellbeing was evaluated through the perception of being heard (Casas y Bello, 2012) and trust in the city council.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Empowering children in politics: evaluating a participative democratic programme

The objective of this study was to evaluate a participative democracy programme called Ágora infantil, carried out with students between the ages of 10 and 12. As in participatory budgets, the process is based on the research-action model (Lewin, 1946) and consists of the city council opening up decision-making on a part of the municipal budget or a concrete policy to the children of the municipality. This process of diagnosis, prioritization and decision-making was completed over the course of 5 to 7 sessions during school hours and implemented by the Coglobal association. Once the participants make a decision, the city council carries out the project selected in the municipality (the decision made is binding). The main goal of Ágora Infantil is to generate psychological empowerment and wellbeing amongst its participants, and to measure the effects of this programme on children’s psychological empowerment. To this end, we used Zimmerman´s model (Zimmerman, 1995; Zimmerman, 2000). The operationalization of the strengthening was based on: 1) knowledge of local politics (as a component of the interactional dimension of psychological empowerment) and 2) the self-perception of being able to influence the future of the municipality (component of the intrapersonal dimension of psychological empowerment). In addition, wellbeing was evaluated through the perception of being heard (Casas y Bello, 2012) and trust in the city council.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Promoción de la condición física y salud a través de la mención de Educación Física: las #Olimprimarias

Póster presentado en: VIII Jornadas de Innovación Docente de la UBU, Burgos, 5 de abril de 2016, organizadas por el Instituto de Formación e Innovación Educativa-IFIE de la Universidad de Burgo

El endomarketing en la estrategia de comunicación en la empresa

Los recursos humanos son una de las mayores bazas para una organización y una de las fuentes más importantes para la obtención de una ventaja competitiva dinámica, de ahí la importancia del análisis de la gestión de este recurso y el estudio de su mejora. Por ello, en este artículo, se analiza la evolución y desarrollo del marketing interno o endomarketing y los diferentes modelos existentes, así como las relaciones entre el marketing interno, el externo, la satisfacción de los clientes, tanto internos como externos y la relación interdepartamental para la consecución de los objetivos de la organización. Gracias al reconocimiento e importancia que ha adquirido el endomarketing en el último cuarto de siglo y tras el análisis de la literatura existente, en este trabajo presentamos un modelo de gestión de marketing interno.Human resources are one of the biggest advantages to an organization and one of the most important sources for obtaining a dynamic competitive advantage, hence the importance of analyzing the resource management and study of their improvement. Therefore, this article examines the evolution and development of internal marketing or endomarketing and the different models, and the relationship between internal marketing, external, customer satisfaction, both internal and external and interdepartmental relationships to achieve the objectives of the organization. To the recognition and importance that it has acquired endomarketing in the last quartercentury after the analysis of existing literature, this paper presents a model of internal marketing management

Un procedimiento nuevo para adaptar cualquier tipo de suelo para la construcción y consolidación de estructuras de tierra: Sistema de Tierra Proyectada

The “projected earth system” is put forward as an alternative construction method. The soil from each site is adapted following a specific protocol to make it suitable for spraying. The type of construction and the receiving surface determine the machinery and spraying system used (dry or wet mix). The result will be similar in texture and colour to the original material (in the case of earth walls) or to the surrounding material.Un procedimiento nuevo para adaptar cualquier tipo de suelo para la construcción y consolidación de estructuras de tierra: Sistema de Tierra Proyectada. Se plantea la “tierra proyectada” como nuevo sistema constructivo. Se adecuará la tierra de cada intervención con un protocolo para poder ser proyectada. El tipo de intervención y el soporte sobre el que se proyectará determinarán la maquinaria y el sistema de proyección (vía seca o húmeda). El resultado tendrá similar textura y color que el soporte restaurado (en muros de tierra) o que el material del entorno (en taludes carreteros u obras de tierra de nueva construcción)