Output
Descriptions of all output files for guild-based analysis of 16S-rRNA sequencing data based on Wu and Zhao et al., 2021.
Output files will be located under the folder /results.
| Subfolder | Description | 16Sguild process (step) |
Tool | Link to Documentation |
|---|---|---|---|---|
/main_results/s1_{base_name}_raw.qzv |
QIIME2 visualization summarizing the quality and distribution of the raw sequencing data before trimming | Quality Check (s2) | QIIME2 | Demux Summarize \ QIIME2 View |
/main_results/s3_{base_name}_trimmed.qzv |
QIIME2 visualization (.qzv) summarizing the quality and distribution of the raw sequencing data after trimming | Trimming (s3) | QIIME2 (cutadapt) | Trimming \ QIIME2 View |
/main_results/MULTIQC |
Folder containing the MultiQC file for all raw samples together. | MultiQC (s0) | MultiQC | MultiQC |
/main_results/MULTIQC_trimmed |
Folder containing the MultiQC file for all trimmed samples together. | MultiQC (s0) | MultiQC | MultiQC |
/main_results/s7_{base_name}_.qzv |
QIIME2 visualization of feature table summary of denoising statistics | Denoise (s5) | 16Sguild | QIIME2 View |
/main_results/s11a_database |
rds file for 16Sguild database assigning UUIDs to ASVs |
Filtering (s12) | Database | Pipeline Feature |
/main_results/s14_alpha-rarefaction.qzv |
QIIME2 visualization of alpha rarefaction | Alpha rarefaction (s14) | QIIME2 | Alpha rarefaction |
/main_results/s17_formatTable |
filtered ASV table | Filtering (s17) | 16Sguild | Pipeline Feature |
/main_results/s20_CAG |
tables and graphs for CAG results | Plot CAG (s20) | 16Sguild | Pipeline Feature |
/intermediate_results/s1 |
import sequencing files into a QIIME 2 artifact (.qza file) | Import (s1) | QIIME2 | Importing data |
/intermediate_results/s2 |
QIIME2 artifact (.qza) summarizing the quality and distribution of the raw sequencing data after trimming | Quality Check (s2) | QIIME2 | Demux Summarize |
/intermediate_results/FASTQC |
Folder containing the FASTQC files for the raw samples | FASTQC (s0) | FASTQC | FASTQC |
/intermediate_results/FASTQC_trimmed |
Folder containing the FASTQC files for the trimmed samples | FASTQC (s0) | FASTQC | FASTQC |
/intermediate_results/s5 |
QIIME2 artifact after completing DADA2 denoising. Visualized in s6 object | Quality filtering (s5) | QIIME2 (DADA2) | DADA2 |
/intermediate_results/s6_{base_name}_group#_denoising-stats.qzv |
Visualization of the denoising results using DADA2 | Denoise (s5) | 16Sguild | DADA2 denoising with QIIME2 \ QIIME2 View |
/intermediate_results/s9 |
converts QIIME2 artifact into FASTA file | Filtering (s12) | 16Sguild | Pipeline Feature |
/intermediate_results/s10 |
Quality filtering (s10) | 16Sguild | Pipeline Feature | |
/intermediate_results/s11b |
UUID and txt files for database | Filtering (s12) | Database | Pipeline Feature |
/intermediate_results/s12 |
Prepare both sequences and feature table into proper QIIME-compatible artifacts | QIIME2 Import (s12) | QIIME2 | Pipeline Feature |
/intermediate_results/s13 |
This set of steps produces a rooted phylogenetic tree (.qza) by aligning representative sequences, filtering the alignment, building an unrooted tree, and then applying midpoint rooting. | (s13) | QIIME2 | QIIME2 phylogenetic tree construction |
/intermediate_results/alphaBetaDiversity |
QIIME2 visualization of beta diversity plots | Diversity analysis (s15) | QIIME2 | Diversity |
/intermediate_results/s15 |
Diversity analysis (s15) | QIIME2 | Diversity | |
/intermediate_results/s16 |
exporting results | Export (s16) | 16Sguild | Pipeline Feature |
/intermediate_results/s19 |
correlation analysis results | Correlation analysis (s19) | FastSpar | FastSpar |