Overview

The Assembly_Fetch workflow downloads assemblies from NCBI. This is particularly useful when you need to align reads against a reference genome, for example during a reference-based phylogenetics workflow. This workflow can be run in two ways:

You can provide an accession for the specific assembly that you want to download, and Assembly_Fetch will run only the NCBI genome download task to download this assembly,
You can provide an assembly, and Assembly_Fetch will first use the ReferenceSeeker task to first find the closest reference genome in RefSeq to your query assembly and then will run the NCBI genome download task to download that reference assembly.

<aside> 💡 NOTE: If using Assembly_Fetch workflow version 1.3.0 or higher, the call-caching feature of Terra has been DISABLED to ensure that the workflow is run from the beginning and data is downloaded fresh. Call-caching will not be enabled, even if the user checks the box ✅ in the Terra workflow interface.

Workflows available

Overview

Inputs

Tasks

Outputs

References