12 papers · ranked by Valyu relevance
Abhinav Sharma, Davi Josué Marcon, Johannes Loubser, Karla Valéria Batista Lima + 2 more
The MTBseq pipeline, published in 2018, was designed to address bioinformatics challenges in tuberculosis research using whole-genome sequencing data. It was the first publicly available pipeline on Github to perform full analysis of whole-genome sequencing (WGS) data for Mycobacterium tuberculosis encompassing quality…
Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala + 3 more
'Daniel Remondini' 'Gastone Castellani' 'Enrico Giampieri'] Background Current high-throughput technologies-i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.-generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several…
Marco Aldinucci, Cristina Calcagno, Mario Coppo, Ferruccio Damiani + 5 more
'Maurizio Drocco' 'Eva Sciacca' 'Salvatore Spinella' 'Massimo Torquati' 'Angelo Troina'] The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the…
Marcin Cieślik, Cameron Mura
Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In…
Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero + 4 more
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data.…
Marek Sztuka, Krzysztof Kotlarz, Magda Mielczarek, Piotr Hajduk + 2 more
This study compared computational approaches to parallelisation of an SNP calling workflow. Data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome, post-alignment, and SNP calling. Three approaches to…
Michael Grauer, Patrick Reynolds, Marion Hoogstoel, Francois Budin + 2 more
'Martin A. Styner' 'Ipek Oguz'] Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that…
Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier + 3 more
We designed a PyQt graphical user interface – Sequanix – aiming at democratizing the use of Snakemake pipelines. Although the primary goal of Sequanix was to facilitate the execution of NGS Snakemake pipelines available in the Sequana project (http://sequana.readthedocs.io), it can also handle any Snakemake pipelines.…
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki + 3 more
'Hikaru Inoue' 'Rui Yamaguchi' 'Satoru Miyano'] Background Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
Jason P. Kurs, Manuele Simi, Fabien Campagne
Computational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed…
Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber + 1 more
'Alper Kucukural'] Background The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and…