QIIME2 workflows

Available workflows

Denoising (using qiime2's dada2 integration for paired / single end data.

Inputs

• Demultiplexed sequences as a qiime2 aertifact file (qza) containing the sequence information.
• Metadata table (tabular)
• Truncation length
• Trimming length (optional)

For the paired end workflow the truncation and trimming length for the reverse reads can / has to be given.

Processing

• Denoising with qiime2 dada2 denoise-single/paired
• For each of the three outputs (see below) another tool is started to prepare a corresponding qzv file
  • representative sequences qiime2 feature-table tabulate-seqs
  • denoising statistics qiime2 metadata tabulate
  • summary of the feature table

Outputs

• representative sequences
• denoising statistics
• summary of the feature table (how many sequences are lost in the corresponding steps)

Changelog

[0.1] 2024-04-08

First release.

[0.2] 2024-05-23

Fix dockstore.yml.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_paired/qiime2__dada2__denoise_paired/2023.5.0+q2galaxy.2023.5.0.2
• toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2023.5.0+q2galaxy.2023.5.0.2
• toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2023.5.0+q2galaxy.2023.5.0.2
• toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2023.5.0+q2galaxy.2023.5.0.2