Output

What this document covers

This page describes the files and directories produced by CholeraSeq. It explains where to find the tree outputs, QC reports, and other important result files.

Result directory structure

By default, the pipeline creates the following top-level directories inside your --outdir:

• fastp/ – trimmed read output and Fastp QC logs
• fastqc/ – FastQC reports for raw or trimmed reads
• snippy/ – snippy individual sample results and consensus FASTA input files
• mask/ – recombination masking outputs from gubbins
• iqtree/ – final tree files and IQ-TREE reports
• multiqc/ – aggregated QC report and plots
• pipeline_info/ – Nextflow and pipeline execution reports
• cat/ / utils/ / python/ / r/ / seqkit/ / run/ – workflow step-specific directories for intermediate outputs

The exact layout may vary depending on which pipeline steps are executed and whether optional modes such as global core alignment are enabled.

Key outputs

Final tree and phylogeny

• iqtree/*.treefile – main maximum likelihood tree file in Newick-like format
• iqtree/*.iqtree – IQ-TREE run summary and model information
• iqtree/*.mldist – likelihood-distance matrix produced by IQ-TREE
• iqtree/*.log – IQ-TREE execution log

These files represent the final phylogeny inferred by CholeraSeq from a recombination-masked core-genome SNP alignment.

Recombination masking

• mask/* – outputs from gubbins and masking scripts
• mask/*.gff – recombination annotation for the input alignment
• mask/*.masked.fasta – recombination-masked alignments used for downstream tree inference

Consensus and alignment inputs

• snippy/* – consensus FASTA files and variant calling outputs from snippy
• snippy/*.vcf – variant call files
• snippy/*.bam – read alignments used to generate consensus sequences
• snippy/*.consensus.fa – per-sample consensus FASTA sequences
• cat/* – concatenated consensus alignments

MultiQC report

• multiqc/multiqc_report.html – interactive summary report for QC and workflow metrics
• multiqc/multiqc_data/ – parsed statistics from supported tools
• multiqc/multiqc_plots/ – static plot images

Workflow metadata

• pipeline_info/execution_report.html – a Nextflow execution report
• pipeline_info/execution_timeline.html – timeline of pipeline processes
• pipeline_info/execution_trace.txt – trace of pipeline tasks
• pipeline_info/pipeline_dag.html – workflow DAG visualization
• pipeline_info/software_versions.yml – list of software versions used in the run
• pipeline_info/samplesheet.valid.csv – cleaned or validated sample sheet used by the pipeline

Interpreting the key tree outputs

The primary phylogeny is stored under iqtree/. Because the pipeline masks recombination and extracts variable sites through varcodons.py, the final tree should be interpreted as a recombination-masked phylogeny derived from a reference-guided core alignment.

For additional detail on the workflow and what each directory contains, see workflow.md.