Optimizing Research Workflows - A Documentation of Snakemake
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Snakemake is a powerful and versatile workflow management system that simplifies the creation, execution, and management of data analysis pipelines. It uses a user-friendly, Python-based language to define workflows, making it particularly valuable for automating and reproducibly managing complex computational tasks in research and data analysis.
Research Software Engineering Training Materials
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An ongoing collection of RSE training material, workshops, and resources. We are compiling this list as a starting point for future activities. We are especially seeking material that goes beyond basic research computing competency (e.g. what The Carpentries does so well) and is general enough to span multiple domains. Specific tools and technologies used only in one domain, or applicable to only one subset of computing (i.e. HPC) are typically too narrowly focused. When in doubt, submit it to be included or reach out and we’d be happy to discuss.
HPCwire
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HPCwire is a prominent news and information source for the HPC community. Their website offers articles, analysis, and reports on HPC technologies, applications, and industry trends.
Recommended Libraries for Cyberinfrastructure Users Developing Jupyter Notebooks
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This repository contains information about Jupyter Widgets and how they can be used to develop interactive workflows, data dashboards, and web applications that can be run on HPC systems and science gateways. Easy to build web applications are not only useful for scientists. They can also be used by software engineers and system admins who want to quickly create tools tools for file management and more!
Bioinformatics Workflow Management with Nextflow
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Nextflow is an open-source, domain-specific language and workflow manager designed for the execution and coordination of scientific and data-intensive computational workflows. It was specifically created to address the challenges faced by researchers and scientists when dealing with complex and scalable computational pipelines, particularly in fields such as bioinformatics, genomics, and data analysis.
Here provided some links to start with.
Samtools Documentation
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Samtools is a suite of programs for interacting with high-throughput sequencing data, especially in the SAM/BAM format. It offers various utilities for processing, analyzing, and managing sequence data generated from next-generation sequencing (NGS) experiments. Samtools is widely used in bioinformatics and genomics research for tasks such as read alignment, variant calling, and data manipulation.