Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines.

Autor:	Federico A; Bioinformatics Program, Boston University, Boston, MA, United States.; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States., Karagiannis T; Bioinformatics Program, Boston University, Boston, MA, United States., Karri K; Bioinformatics Program, Boston University, Boston, MA, United States., Kishore D; Bioinformatics Program, Boston University, Boston, MA, United States., Koga Y; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States., Campbell JD; Bioinformatics Program, Boston University, Boston, MA, United States.; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States., Monti S; Bioinformatics Program, Boston University, Boston, MA, United States.; Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2019 Jun 28; Vol. 10, pp. 614. Date of Electronic Publication: 2019 Jun 28 (Print Publication: 2019).
DOI:	10.3389/fgene.2019.00614
Abstrakt:	The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data preprocessing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, as well as digital gene expression data. This report highlights the design methodology behind Pipeliner that enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments. We also provide a quick start user guide demonstrating how to setup and execute available pipelines with toy datasets.
Databáze:	MEDLINE
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