Workflow Catalog

Hutch Data Core

Updated: April 22, 2021

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The Hutch Data Core works to support researchers by providing access to a set of curated bioinformatics workflows which automate commonly-needed tasks.

We are in the process of expanding this catalog of workflows, and we are actively soliciting input from researchers who have an interest in adding workflow automation to their ongoing projects.

Because of our extensive work with the Microbiome Research Initiative, many of the workflows listed below are designed for the analysis of microbial sequence data. However, the goal of this catalog is to be comprehensive and not specific to any single scientific domain.

If you are interested in adding a workflow to this catalog which meets your needs, please don’t hesitate to get in touch.

Workflow Support

By including a workflow in this catalog, the Data Core is committed to helping individual researchers as they implement the workflow on their own datasets. This may include consultation on the proper use of a workflow, helping to set up an initial test run, as well as troubleshooting errors which may come up. By creating a catalog of well-supported workflows, we hope to streamline the data analysis process for future researchers who will be able to take advantage of the enhanced documentation and debugging that results from our efforts.

Please reach out if you have questions about the use of any workflows listed below, or would like to see an additional use-case supported.

Workflows

Each of the workflows below have a short description and a link to the repository which should contain documentation on how to run the workflow. If any of these materials are insufficient, we are extremely interested in working to make improvements and would appreciate your feedback.

ccs-nf

Purpose: Extract CCS from CLR data generated by the PacBio Sequel instrument Homepage: https://github.com/FredHutch/ccs-nf

geneshot

Purpose: Perform gene-level metagenomic analysis of WGS datasets for strain-level microbiome analysis Homepage: https://github.com/Golob-Minot/geneshot

multi-fastqc-nf

Purpose: Generate a QC summary over a collection of FASTQ input files Homepage: https://github.com/FredHutch/multi-fastqc-nf

nf-anvio-pangenome

Purpose: Analyze a set of microbial genomes with the anvi’o pangenome pipeline Homepage: https://github.com/FredHutch/nf-anvio-pangenome

PGAP-nf

Purpose: Annotate a set of bacterial genomes using the PGAP annotation software suite Homepage: https://github.com/FredHutch/PGAP-nf

prokka-nf

Purpose: Annotate a set of bacterial genomes using the Prokka annotation software suite Homepage: https://github.com/FredHutch/prokka-nf

unicycler-nf

Purpose: Perform de novo assembly of bacterial genomes using the UniCycler hybrid assembler Homepage: https://github.com/FredHutch/unicycler-nf

Updated: April 22, 2021

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