Page Contents

Workflows available

BaseSpace_Fetch

Cauris_CladeTyper

Concatenate_Column_Content

Create_Terra_Table

Find_Shared_Variants

Freyja Workflow Series

Mercury_Prep_N_Batch

NCBI-AMRFinderPlus

Pangolin Update

Samples_to_Ref_Tree

Snippy_Streamline

Snippy_Streamline_FASTA

Snippy_Variants

TBProfiler_tNGS

TheiaCoV Workflow Series

TheiaProk Workflow Series

Transfer_Column_Content

Zip_Column_Content

Overview

RASUSA functions to randomly downsample the number of raw reads to a user-defined threshold.

📋 Use Cases:

to reduce computing resources when samples end up with drastically more data than needed to perform analyses
to perform limit of detection (LOD) studies to identify appropriate minimum coverage thresholds required to perform downstream analyses

🔧 Desired size may be specified by inputting any one of the following:

coverage (e.g. 20X)
number of bases (e.g. ”5m” for 5 megabases)
number of reads (e.g. 100000 total reads)
fraction of reads (e.g. 0.5 samples half the reads)

<aside> 💡 NOTE

If using RASUSA_PHB workflow version v2.0.0 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.

</aside>

Inputs

Input all String values (other than when selecting dropdown option Strings) in quotations, e.g. “5m”

Required Inputs

Optional Inputs

Outputs

💡 Don’t Forget! Remember to use the subsampled reads in downstream analyses with this.read1_subsampled and this.read2_subsampled inputs.

✅ Verify reads were successfully subsampled before downstream analyses by comparing read file size/s to the original read file size/s

View file sizes by clicking on the read file listed in the Terra data table and looking at the file size

Terra Outputs

References

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