Feridun Mert Celebi, Elizabeth A. McDaniel, and Taylor Reiter
Published: Mar 07, 2023
A workflow orchestration framework can streamline repeatable tasks and make workflows broadly usable. From several options, we chose Nextflow due to the ease of deploying across platforms, vibrant nf-core community, and ability to manage and monitor workflows with Nextflow Tower.
Adair L. Borges, Rachel J. Dutton, Elizabeth A. McDaniel, Taylor Reiter, and Emily C.P. Weiss
Published: Mar 11, 2023
How do you approach getting a microbiome set up in a new lab? We’re sharing protocols for how we collected, stocked, and sequenced a set of cheese rind microbiomes and generated a high-quality metagenomics resource for future computational studies.
We want to swiftly generate genome assemblies and produce quality-control statistics to gauge the need for more curation. We built a Nextflow pipeline that assembles PacBio HiFi reads from a single organism and runs QC checks on the resulting assembly.
We want to seamlessly process and summarize metagenomics data from Illumina or Nanopore technologies. We built a Nextflow workflow that handles common metagenomics tasks and produces useful outputs and intuitive visualizations.