BigBacter

BigBacter is a pipeline aimed at simplifying bacterial genomic surviellance. This is accomplished by:

1. pre-clustering isolates into closely related subtypes prior to phylogenetic analysis
2. automatically selecting and archiving cluster-specific reference genomes for SNP analysis
3. identifying and excluding low quality samples
4. archiving samples and automatically including them when samples from the same cluster are identified
5. re-using archived alignment files, thus greatly increasing the speed of SNP analysis
6. automatically generating figures needed for phylogenetic analysis (i.e., trees and SNP matrices)

Please see the wiki for more information.

BigBacter was originally written by Jared Johnson for the Washington State Department of Health.

Quick Start

1. Configure all pre-made PopPUNK databases (Performed once):

⚠️ This downloads PopPUNK databases for 23 bacterial species (~21 GB total; ~2 hours using AWS Batch). See the wiki page for how to prepare individual PopPUNK databases.

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile singularity,all_dbs \
    -entry PREPARE_DB \
    --db $PWD/db \
    --max_cpus 4 \
    --max_memory 8.GB

2. Prepare your samplesheet (Performed each time):

sample,taxa,assembly,fastq_1,fastq_2
sample1,Acinetobacter_baumannii,sample1.fasta,sample1_R1.fastq.gz,sample1_R2.fastq.gz
sample2,Escherichia_coli,sample2.fasta,sample2_R1.fastq.gz,sample2_R2.fastq.gz
sample3,Staphylococcus_aureus,sample3.fasta,sample3_R1.fastq.gz,sample3_R2.fastq.gz

3. Running BigBacter (Performed each time):

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile singularity \
    --input $PWD/samplesheet.csv
    --db $PWD/db \
    --outdir $PWD/results \
    --max_cpus 4 \
    --max_memory 8.GB

4. Add the new samples to your database (Performed each time):

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile singularity \
    --input $PWD/samplesheet.csv
    --db $PWD/db \
    --outdir $PWD/results \
    --max_cpus 4 \
    --max_memory 8.GB \
    --push true \
    -resume