Config

prefix

The prefix determines the name of the output folder created under results/.

For example: prefix: 2026-06-04_Project_IMPALA_run3_SNPkitv2

will generate outputs under: results/2026-06-04_Project_IMPALA_run3_SNPkitv2/

read_input_type

SNPmake supports two read input modes: read_input_type: raw

or read_input_type: trimmed

If using raw reads, SNPkit expects files named: {sample_id}_R1.fastq.gz{sample_id}_R2.fastq.gz

If using trimmed reads, SNPkit expects files named: {sample_id}_R1_trim_paired.fastq.gz{sample_id}_R2_trim_paired.fastq.gz

When read_input_type: trimmed, reads are passed directly to the alignment step and do not go through the trimming or downsampling rules.

When read_input_type: raw, reads are passed through trimming and downsampling before alignment.

workflow_mode

SNPmake currently supports two run modes: workflow_mode: vcf_only

or workflow_mode: full

vcf_only generates the core SNP/indel VCF outputs.

full generates VCFs, masking files, consensus sequences, and the final reference-based alignment.

Reference genome

Set the reference genome and reference contig: reference_genome: /path/to/reference.fastareference_contig: reference_contig_name

The reference_contig should match the FASTA record ID used for the main reference sequence.

Existing MSA

If you have an existing reference-coordinate MSA and want to merge new samples into it, provide the path using: existing_msa: /path/to/existing_alignment.faexisting_msa_ref_id: reference_contig_nameexisting_msa_duplicate_policy: error

If you do not have an existing MSA, leave this blank: existing_msa:

When an existing MSA is provided, SNPmake checks that the reference sequence in the existing MSA matches the provided reference_genome. If the references do not match, the workflow will stop rather than merging incompatible coordinate systems.

Plasmid/phage masking mode

To skip phage masking, use: plasmid_variant_calling: truephastest_results:

To enable phage masking, use: plasmid_variant_calling: falsephastest_results: /path/to/phastest_results_directory

When phage masking is enabled, the phastest_results directory must contain: predicted_phage_regions.json