Analyzing the differences between reads and contigs when performing a taxonomic assignment comparison in metagenomics

Metagenomics is an inherently complex field in which one of the primary goals is to determine the compositional organisms present in an environmental sample. Thereby, diverse tools have been developed that are based on the similarity search results obtained from comparing a set of sequences against a database. However, to achieve this goal there still are affairs to solve such as dealing with genomic variants and detecting repeated sequences that could belong to different species in a mixture of uneven and unknown representation of organisms in a sample. Hence, the question of whether analyzing a sample with reads provides further understanding of the metagenome than with contigs arises. The assembly yields larger genomic fragments but bears the risk of producing chimeric contigs. On the other hand, reads are shorter and therefore their statistical significance is harder to asses, but there is a larger number of them. Consequently, we have developed a workflow to assess and compare the quality of each of these alternatives. Synthetic read datasets beloging to previously identified organisms are generated in order to validate the results. Afterwards, we assemble these into a set of contigs and perform a taxonomic analysis on both datasets. The tools we have developed demonstrate that analyzing with reads provide a more trustworthy representation of the species in a sample than contigs especially in cases that present a high genomic variability.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Workflows and service discovery: a mobile device approach

Bioinformatics has moved from command-line standalone programs to web-service based environments. Such trend has resulted in an enormous amount of online resources which can be hard to find and identify, let alone execute and exploit. Furthermore, these resources are aimed -in general- to solve specific tasks. Usually, this tasks need to be combined in order to achieve the desired results. In this line, finding the appropriate set of tools to build up a workflow to solve a problem with the services available in a repository is itself a complex exercise. Issues such as services discovering, composition and representation appear. On the technological side, mobile devices have experienced an incredible growth in the number of users and technical capabilities. Starting from this reality, in the present paper, we propose a solution for service discovering and workflow generation while distinct approaches of representing workflows in a mobile environment are reviewed and discussed. As a proof of concept, a specific use case has been developed: we have embedded an expanded version of our Magallanes search engine into mORCA, our mobile client for bioinformatics. Such composition delivers a powerful and ubiquitous solution that provides the user with a handy tool for not only generate and represent workflows, but also services, data types, operations and service types discoveryUniversidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Methods and workflows for the taxonomic analysis of metagenomic data

Todas las plantas y animales tienen comunidades microbianas estrechamente asociadas que hacen que los nutrientes, metales y vitaminas necesarios estén disponibles para su huésped, contribuyendo esencialmente a la vida en la Tierra. El campo inherentemente complejo que tiene como objetivo comprender las contribuciones de estas microbiotas a la biósfera se conoce como metagenómica. Uno de los principales objetivos en este campo de investigación es determinar la composición de los organismos presentes en una muestra ambiental. Para ello, se han desarrollado diversas herramientas, la mayoría de ellas basadas en los resultados de búsqueda de similitud obtenidos al comparar un conjunto de secuencias biológicas contra una base de datos. Aunque el campo ha avanzado significativamente desde su inicio, todavía hay otros asuntos por resolver como tratar con variantes genómicas y detectar secuencias repetidas que podrían pertenecer a diferentes especies en una mezcla de organismos desiguales y desconocidos. Los distintos enfoques al analizar una muestra de metagenoma dan lugar a preguntarse si el análisis de una muestra con lecturas (fragmentos cortos de ADN producto de procedimientos de secuenciación) proporciona una mayor comprensión del metagenoma que con contigs (lecturas superpuestas que se han ensamblado juntas). El ensamblaje produce fragmentos genómicos más grandes, pero conlleva el riesgo de producir contigs a partir de lecturas de diferentes organismos. Por otro lado, las lecturas son más cortas y por ello su significación estadística es más difícil de evaluar, pero son más numerosas. En este proyecto, evaluamos y comparamos la calidad de cada una de estas alternativas para establecer el enfoque de datos que proporciona los mejores resultados en términos de informar la abundancia relativa de especies dentro de una muestra..