Inputs

Below is a summary and description of each input parameter.

Table of contents

1. All Input Options
2. --input
3. --ncbi
4. --db
5. --push
6. --max_depth
7. --min_genfrac
8. --max_lowcov
9. --max_het
10. --strong_link_cutoff
11. --inter_link_cutoff
12. --partition_threshold
13. --max_static
14. --max_ml
15. --min_tree
16. --db_info
17. --resolve_merged
18. --run_id

---

All Input Options

// Input options
input                      = "${projectDir}/assets/samplesheet.csv"
ncbi                       = null
db                         = null
push                       = false

// QC: Reads & Assembly
read_qc                    = true
assembly_qc                = true
min_contig_len             = 300

// QC: Variant Calling
max_depth                  = 100
min_genfrac                = 85
max_lowcov                 = 5
max_het                    = 1

// Tree options
max_ml                     = 500
min_tree                   = 2

// Reporting options
strong_link_cutoff         = 10
inter_link_cutoff          = 50
partition_threshold        = 100
max_static                 = 100

// Other options (caution)
db_info                    = true
resolve_merged             = true
run_id                     = null

--input

Path to a comma-separated file containing information about PopPUNK databases or samples. An absolute path to the file should be used.

PopPUNK database sheet example

pp_db_list.csv:

taxa,pp_db
Acinetobacter_baumannii,abaumannii_db.tar.gz
Escherichia_coli,ecoli_db.tar.bz2
Staphylococcus_aureus,staph_db/

Samplesheet example

samplesheet.csv:

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

--ncbi

Path to a comma-separated file containing information for samples that should be pulled from NCBI.

sample,taxa,assembly,sra
SAMN12769618,Acinetobacter_baumannii,GCF_008632635.1,SRR11176973

--db

Path to the BigBacter database. It is recommended that PopPUNK databases be configured to a single common directory (i.e., the BigBacter database). This database can be set up automatically using the PREPARE_DB workflow (-entry PREPARE_DB).

--push

Tells the pipeline whether you want to save (i.e., “push”) new samples to the BigBacter database (default: false). It is recommended that you check results prior to pushing files. Once confirmed, files can be pushed using --push true and -resume.

--max_depth

Maximum read depth per sample (default: 100). This is used by Snippy to randomly subsample reads.

--min_genfrac

Minimum percent of the reference genome that a sample must contain for it to be included in the core SNP analysis (default: 85).

--max_lowcov

Maximum percent of low coverage sites allowed for a sample to be included in the core SNP analysis (default: 5).

--max_het

Maximum percent of heterogeneous sites allowed for a sample to be included in the core SNP analysis (default: 1). Given that bacteria are haploid, the presence of heterogeneous sites indicates either contamination or unrepresented homologs.

--strong_link_cutoff

SNP distance threshold used to classify strong genomic linkages (default: 10). This has no impact on core SNP analysis and is only meant to aid interpretation of genetic linkages.

--inter_link_cutoff

SNP distance threshold used to classify intermediate genomic linkages (default: 50). This has no impact on core SNP analysis and is only meant to aid interpretation of genetic linkages.

--partition_threshold

Number of estimated nucleotide substitutions used to partition samples in maximum likelihood trees using cutree and hclust (default: 100).

--max_static

Maximum number of samples included in a static image (i.e., .jpg). Static images will not be generated for clusters containing more samples than this value.

--max_ml

Maximum number of samples that a cluster can contain for maximum likelihood tree generation (default: 500). If the number of samples exceeds this threshold, BigBacter will switch to the neighbor-joining approach.

--min_tree

Minimum number of samples in a cluster for a tree to be produced, excluding the reference genome (default: 2). This must be greater than 2 or IQTREE will fail.

--db_info

Provides a summary of your BigBacter database (default: true). A short summary will be printed to the screen upon completion of the pipeline and a full summary can be found in the run directory (e.g., ${timestamp}-db-info.csv).

--resolve_merged

Whether merged PopPUNK clusters should be resolved (default: true).

Only turn this off if you know what you are doing.

--run_id

Will be used in place of the timestamp ID.

Misuse could lead to database corruption.