Downloads¶

Get run3 denoising files¶

Dada2 outputs

seqs_run3.qza
dada2_stats_run3.qza
base-transition-stats_run3.qza

Move into the dada2 directory in the decomp_tutorial

cd /scratch/alpine/$USER/decomp_tutorial/dada2

Copy the files into your dada2 directory

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/seqs_run3.qza .

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/dada2_stats_run3.qza .

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/base-transition-stats_run3.qza .

Copy over the denoising stats

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/dada2_stats_run3.qzv .

Get the merged table

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/table.qza .

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/table_dada2_visual_summary.qzv .

Get the merged sequences

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/seqs.qza .

cp /pl/active/courses/2026_summer/CSU_2026/q2_workshop_final/QIIME2/dada2_2026/seqs.qzv .

Decomp Tutorial Data Files¶

The following files are used throughout the workshop and are available on Alpine HPC:

File	Alpine Path	Description
`manifest_run2.txt`	`QIIME2/manifest_run2.txt`	Run 2 import manifest
`manifest_run3.txt`	`QIIME2/manifest_run3.txt`	Run 3 import manifest
`metadata_q2_workshop.txt`	`QIIME2/metadata_q2_workshop.txt`	Full sample metadata
`metadata_q2_workshop_noECs.txt`	`QIIME2/metadata_q2_workshop_noECs.txt`	Metadata without environmental controls
`2024.09.backbone.v4.nb.qza`	`QIIME2/2024.09.backbone.v4.nb.qza`	GreenGenes2 V4 Naive Bayes classifier
`2022.10.backbone.sepp-reference.qza`	`QIIME2/2022.10.backbone.sepp-reference.qza`	GreenGenes2 SEPP reference
`tree_gg2.qza`	`QIIME2/tree_gg2.qza`	Pre-built phylogenetic tree
`visualizations.Rmd`	`R/visualizations.Rmd`	R Markdown analysis script
`R.Rproj`	`R/R.Rproj`	RStudio project file