Quick Start

BigBacter requires Nextflow and one of the following container engines: Docker, Podman, Apptainer, Singularity.

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1. Create your samplesheet

The taxa, assembly, fastq_1, and fastq_2 columns are optional — leave them empty if the data is unavailable.

samplesheet.csv:

sample,fastq_1,fastq_2,taxa,assembly
sample1,sample1_R1.fastq.gz,sample1_R2.fastq.gz,Staphylococcus aureus,sample1.fasta
sample2,sample2_R1.fastq.gz,sample2_R2.fastq.gz,Escherichia coli,sample2.fasta
sample3,,,Klebsiella pneumoniae,sample3.fasta
sample4,sample4_R1.fastq.gz,sample4_R2.fastq.gz,,
sample5,,,,

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2. Run BigBacter

It is no longer necessary to configure a species-specific database before running BigBacter.

nextflow run NW-PaGe/BigBacter \
    -r main \
    -profile docker \
    --input $PWD/samplesheet.csv \
    --outdir $PWD/results

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3. Review your results

Results are saved to a timestamped subdirectory within --outdir (e.g., ${outdir}/${timestamp}). See the outputs page for details.

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4. Push your results

Once satisfied with your results, push them to your BigBacter database (set with --db). This saves the results so they are included in future runs. Use --resume to avoid recomputing results from step 2.

nextflow run NW-PaGe/BigBacter \
    -r main \
    -profile docker \
    --input $PWD/samplesheet.csv \
    --outdir $PWD/results \
    --push true \
    --resume

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🔍 Want to learn more? Check out the Getting Started and Overview pages.