11 papers · ranked by Valyu relevance
Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele
Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of…
Menachem Sklarz, Michal Gordon, Vered Chalifa-Caspi
Bioinformatics workflows (WFs) in general, and those involving High Throughput Sequencing data in particular, typically involve executing a sequence of programs on raw sequence files from as many as thousands of samples. Management of these WFs is laborious and error-prone. We have developed NeatSeq-Flow, a python…
Weizhong Li
In recent years, high throughput next generation omics data have been broadly used in many research fields. However, analyzing omics data is still very challenging, especially for researchers with less experience in bioinformatics, software, and programming. Omics data analysis workflows usually are composed of many…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Taylor Reiter, Phillip T. Brooks, Luiz Irber, Shannon E.K. Joslin + 4 more
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter…
Andrew E. Webb, Scott W. Wolf, Ian M. Traniello, Sarah D. Kocher
The exponential growth in biological data generation has created an urgent need for efficient, reproducible computational analysis workflows. Here, we present pipemake, a computational platform designed to streamline the development and implementation of efficient and reproducible Snakemake workflows. pipemake creates…
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang + 1 more
Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution…
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…
Soumitra Pal, Teresa M. Przytycka
Large-scale data analysis in Bioinformatics requires executing several software in a pipelined fashion. Generally each stage in a pipeline takes considerable computing resources and several workflow management systems (WMS), e.g., Snakemake and Nextflow, have been developed to ensure in case of multiple invocation of…
Michael J. Jackson, Edward Wallace, Kostas Kavoussanakis
Workflow management systems represent, manage, and execute multi-step computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed…