<i>nf-core</i>: Community curated bioinformatics pipelines

Ewels, Philip; Peltzer, Alexander; Fillinger, Sven; Alneberg, Johannes; Patel, Harshil; Wilm, Andreas; Garcia, Manon; Tommaso, Paolo Di; Nahnsen, Sven

doi:10.1101/610741

Cited by 78 publications

(73 citation statements)

References 21 publications

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“…To this end, we will continue to improve the usability and portability of our data analysis workflows and will make them available via community efforts such as the nf-core [17] repository. Researchers interested in contributing their datasets to the eQTL Catalogue should contact us at eqtlcatalogue@ebi.ac.uk.…”

Section: Discussionmentioning

confidence: 99%

“…We performed extensive quality control of genotypes (see Methods) and imputed them to the 1000 Genomes Phase 3 [16] reference panel. For RNA sequencing data, we started with the nf-core [17] RNA-seq pipeline written in the Nextflow [18] framework and modified it to support the quantification of four different molecular phenotypes: gene expression, exon expression [19], transcript usage, and promoter, splicing and 3ʹ end usage events defined by txrevise [15] ( Supplementary Figure 3). Using the same quantification workflow ensured that molecular phenotype identifiers (genes, transcripts, exons and events) were consistent between individual studies.…”

Section: Data Analysis Workflowmentioning

confidence: 99%

“…We quantified transcription at four different levels: (1) gene expression, (2) exon expression, (3) transcript usage and (4) transcriptional event usage. Quantification was performed with a Nextflow-based [18] pipeline that we developed by adding new quantification methods to nf-core rnaseq pipeline [17]. Before quantification, we used Trim Galore v0.5.0 to remove sequencing adapters from the fastq files.…”

Section: Rna-seq Datamentioning

confidence: 99%

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eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

Kerimov

Hayhurst

Manning

et al. 2020

Preprint

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An increasing number of gene expression quantitative trait locus (QTL) studies have made summary statistics publicly available, which can be used to gain insight into human complex traits by downstream analyses such as fine-mapping and colocalisation. However, differences between these datasets in their variants tested, allele codings, and in the transcriptional features quantified are a barrier to their widespread use. Here, we present the eQTL Catalogue, a resource which contains quality controlled, uniformly re-computed QTLs from 19 eQTL publications. In addition to gene expression QTLs, we have also identified QTLs at the level of exon expression, transcript usage, and promoter, splice junction and 3ʹ end usage. Our summary statistics can be downloaded by FTP or accessed via a REST API and are also accessible via the Open Targets Genetics Portal. We demonstrate how the eQTL Catalogue and GWAS Catalog APIs can be used to perform colocalisation analysis between GWAS and QTL results without downloading and reformatting summary statistics. New datasets will continuously be added to the eQTL Catalogue, enabling systematic interpretation of human GWAS associations across a large number of cell types and tissues. The eQTL Catalogue is available at https

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Section: Discussionmentioning

confidence: 99%

Section: Data Analysis Workflowmentioning

confidence: 99%

Section: Rna-seq Datamentioning

confidence: 99%

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eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

Kerimov

Hayhurst

Manning

et al. 2020

Preprint

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“…On the other hand, the use of a reference genome to align the reads instead of following a de novo approach could mask some real genetic differences. In this sense, initiatives in nf-core are trying to provide best practice pipelines for the analysis of SARS-CoV-2 data in a peer-reviewed platform that includes some pipelines developed by the Bioinformatics Unit of the Instituto de Salud Carlos III [26][27][28][29]. Moreover, due to the public health threat caused by SARS-CoV-2, more genomic and epidemiologic data are generated every day and the results obtained in the present study should be seen as an early report about the current situation at the end of March 2020.…”

Section: Discussionmentioning

confidence: 99%

Phylodynamics of SARS-CoV-2 transmission in Spain

Fuertes

Caballero

Monzón

et al. 2020

Preprint

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Objectives. SARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe. Methods. Maximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2. Results. Phylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai. Conclusions. Multiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.

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“…Further, NextFlow allows in-line process definition that simplifies the incorporation of small processes that implement new functionality. Not surprisingly, NextFlow has quickly gained popularity, as reflected by several efforts to provide curated and revisioned NextFlow-based pipelines such as nf-core, Pipeliner (18) and CHIPER (19), which are available from a public repository (20).…”

Section: Introductionmentioning

confidence: 99%

DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

Yukselen

Turkyilmaz

Öztürk

et al. 2019

Preprint

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Several platforms currently exist for the design and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, these platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, Nextflow was implemented to simplify portable, scalable, and reproducible scientific pipelines using containers. We have used Nextflow capabilities as leverage and developed a user interface, DolphinNext, for creating, deploying, and executing complex Nextflow pipelines for high throughput data processing. The guiding principle of DolphinNext is to facilitate the building and deployment of complex pipelines using a modular approach implemented in a graphical interface. DolphinNext provides: 1. A drag and drop user interface that abstracts pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. A user interface to monitor pipeline execution that allows the re-initiation of pipelines at intermediate steps 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Seamless portability to distributed computational environments such as high-performance clusters or cloud computing environments.

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nf-core: Community curated bioinformatics pipelines

Cited by 78 publications

References 21 publications

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

Phylodynamics of SARS-CoV-2 transmission in Spain

DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

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