10 papers · ranked by Valyu relevance
Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath + 39 more
Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line solutions such as Nextflow and Snakemake. We report on recent developments in the nf-core and Nextflow…
Xinming Zhuo, Nicholas Renzette, Gregory Omerza
To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across various computational platforms through the implementation of…
Jacopo Tartaglia, Mario Giorgioni, Luigi Cattivelli, Primetta Faccioli
Advances in high-throughput DNA sequencing technologies have dramatically reduced the time and cost required to generate genomic data. As sequencing is no longer a limiting factor, increasing attention must be paid to optimizing the analyses of the large-scale datasets produced. Efficient processing of such data is…
Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber + 1 more
The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets…
Lukas Forer, Sebastian Schönherr
Nextflow has emerged as a flexible and scalable workflow system for building computational pipelines in life sciences. Simultaneously, Software-as-a-Service platforms enable researchers to concentrate on data analysis rather than on setting up pipelines locally. However, converting existing pipelines into web services…
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…
D. Jothi
GTEx_Pro is a Nextflow-based pipeline for preprocessing GTEx v8 transcriptomic data, enhancing multi-tissue comparability. It integrates TMM + CPM normalization and SVA batch effect correction to improve biological signal recovery while reducing systematic variations across 54 GTEx tissues. Designed for scalability and…
Lukas Forer, Sebastian Schönherr
The workflow management system Nextflow builds together with the nf-core community an essential ecosystem in Bioinformatics. However, ensuring the correctness and reliability of large and complex pipelines is challenging, since a unified and automated unit-style testing framework specific to Nextflow is still missing.…
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…
M. Asaduzzaman Prodhan, Matthew Power, Monica Kehoe
Sequencing of a Polymerase Chain Reaction product (amplicon) is called amplicon sequencing. Amplicon sequencing allows for reliable identification of an organism by amplifying, sequencing, and analysing a single conserved marker gene or DNA barcode. As this approach generally involves a single gene, it is a…