Parameters
This document provides an overview of the customizable parameters for the CHOLERASEQ pipeline. Each parameter is listed with its default value, description.
💡 Hint: you may check a full parameters reference file.
Common Parameters
Input Samplesheet
| Parameter | Default Value | Description |
|---|---|---|
input |
null |
The input CSV file containing sample information. |
💡 Hint: The samplesheet should include the columns
[sample,fastq_1,fastq_2].
Output Directory
| Parameter | Default Value | Description |
|---|---|---|
outdir |
null |
The directory where all output files will be written. |
Quality Control Parameters
⚠️ Attention: Ensure these values are adjusted based on the quality of your input data to avoid processing errors. The defaults are set to faciliate a majority of users. Only advanced users are recommended to change these.
| Parameter | Default Value | Description |
|---|---|---|
min_trim_quality |
20 | Fastq reads mean quality threshold 20 fastp |
min_trim_length |
50 | Fastq read minimum trim length 50 fastp |
min_mapping_quality |
20 | minimum mapping quality 20 samtools consensus samtools –min-MQ |
min_base_quality |
20 | minimum base quality 20 samtools consensus samtools –min-BQ |
min_site_coverage |
5 | mimimum site coverage 5 samtools consensus + snippy samtools –min-depth 5; snippy –mincov 5 |
min_allele_fraction |
0.75 | minimum fraction supporting allele call 0.75 samtools consensus + snippy samtools -c 0.75; snippy –minfrac 0.75 |
max_missing_percentage |
50 | Percentage of missing data allowed in a sample before it is excluded from the analysis. max_missing_percentage 0.5 seqcleaner, gubbins max percentage of undefined sites in any consensus fasta sequence |
min_parsimony_coverage |
0.7 | varcodons.py pi job minimum site coverage for varcodons to keep site when generating pi output |
Skipping Pipeline Steps
| Parameter | Default Value | Description |
|---|---|---|
skip_clustering |
false |
Indicate whether you wish to enable the clustering anlysis. |
skip_fastbaps |
true |
Indicate whether to skip fastbaps or not. |
💡 Hint: Use these flags to customize the pipeline execution based on your specific requirements.
Reference Files
| Parameter | Default Value | Description |
|---|---|---|
ref_genbank |
GCF_003063785.full.gbk |
Path to the reference GENBANK file |
⚠️ Warning: It is recommended to use the provided reference files to ensure compatibility with the global core alignment.
Alignment Files
| Parameter | Default Value | Description |
|---|---|---|
global_core_alignment |
null |
Path to the existing global core alignment fasta file. We publish such an alignment on https://doi.org/10.5281/zenodo.10984554 |
cohort_core_alignment |
null |
Path to an existing cohort_core_alignment fasta file. |