Parameters
Descriptions of all input parameters for guild-based analysis of 16S-rRNA sequencing data based on Wu and Zhao et al., 2021.
| Parameter | Description | 16Sguild process (step) |
Tool | Link to Documentation |
|---|---|---|---|---|
samplesheet |
Path to the CSV file containing sample information | Sample manifest import (s1) | QIIME2 import | Importing data |
base_name |
String identifying the name of input folder | General | 16Sguild | Pipeline Feature |
input_type |
Semantic type required for the QIIME2 import function | Import (s1) | QIIME2 import | Importing data |
input_format |
Format of the data to import (e.g., "PairedEndFastqManifestPhred33") | Import (s1) | QIIME2 import | Importing data - Format |
trim_forward |
Forward primer sequence to trim | Trimming (s3) | QIIME2 (cutadapt) | Trimming |
trim_reverse |
Reverse primer sequence to trim | Trimming (s3) | QIIME2 (cutadapt) | Trimming |
metadata |
Path to the sample metadata table (TSV format) | Metadata import (s5) | QIIME2 metadata | Metadata |
trunc_forward |
Position at which to truncate forward reads in QIIME2 DADA2 | Quality filtering (s5) | QIIME2 (DADA2) | DADA2 |
trunc_reverse |
Position at which to truncate reverse reads in QIIME2 DADA2 | Quality filtering (s5) | QIIME2 (DADA2) | DADA2 |
s5_forceDenoiseAll |
(Optional) Force all samples in one denoising step. Default is false. | Denoise (s5) | 16Sguild | Pipeline Feature |
seed |
(Optional) Random seed for various steps in 16SguildR. Default is 42. |
Quality filtering (s10) | 16Sguild | Pipeline Feature |
num_replicates |
(Optional) Involved with filtering out unreliable sequences. Default is 1000. | Quality filtering (s10) | 16Sguild | Pipeline Feature |
linkage_table |
Table output from 16Sguild database assigning UUIDs to ASVs | Filtering (s12) | Database | Pipeline Feature |
max |
Maximum depth value used for alpha rarefaction | Alpha rarefaction (s14) | QIIME2 | Alpha rarefaction |
min |
(Optional) Minimum depth value used for alpha rarefaction. Default is 100. | Alpha rarefaction (s14) | QIIME2 | Alpha rarefaction |
steps |
(Optional) Number of intermediate depths for alpha rarefaction visualization. Default is 100. | Alpha rarefaction (s14) | QIIME2 | Alpha rarefaction |
sampling_depth |
Rarefaction sampling depth for diversity analysis | Diversity analysis (s15) | QIIME2 | Diversity |
exclude_iterations |
(Optional) Number of times highly correlated OTU pairs are discovered and excluded in SparCC analysis. Default is 20. | Correlation analysis (s19) | FastSpar | FastSpar |
iterations |
(Optional) Number of SparCC correlation estimations. Default is 50. | Correlation analysis (s19) | FastSpar | FastSpar |
threshold |
(Optional) Minimum threshold to exclude correlated OTU pairs in SparCC analysis. Default is 0.2. | Correlation analysis (s19) | FastSpar | FastSpar |
number_bootstrap |
(Optional) Number of bootstraps for permutation based p-value estimations. Default is 1000. | Correlation analysis (s19) | FastSpar/rmcorr | FastSpar |
permutations |
(Optional) Number of correlations for each bootstrap count. Default is 1000. | Correlation analysis (s19) | FastSpar | FastSpar |
s19_rmcorr |
(Optional) Run rmcorr for repeated measures correlation. Default is false. Requires subject_column. |
Correlation analysis (s19) | rmcorr | RMcorr |
subject_column |
(Optional) Label for sample type. Default is 'subject'. |
Correlation analysis (s19) | rmcorr | RMcorr |
nfiles_input |
(Optional) Number of top individual CAG plots to generate. Default is 5. | Plot CAG (s20c) | 16Sguild | Pipeline Feature |
outdir |
(Optional) Name of folder where the results will be stored. Default is 'results'. |
General | Nextflow | Nextflow |
publish.mode |
(Optional) Default to 'symlink', but can be changed to 'copy' if necessary. |
General | Nextflow | Nextflow |