Illumina WGS

PFsnake

P. falciparum pipeline for variant calling, CNV and drug-resistance summaries.

STATUS: TEST IN PROGRESS

Pipeline Flow

Prefilter→ fastp→ BWA / BAM QC→ GATK / Variants→ CNV→ Mixed Infection→ Drug Resistance

Build

cd PFsnake
docker build -t pf-snake:1.0 .

Run

./PFsnake/Go_PFsnake.sh \
  -i /path/to/fastq \
  -o /path/to/output \
  -d /path/to/ref.fasta \
  -p 2 \
  -K

Real Example

Go_PFsnake.sh \
  -i PFsnake/20261101_PF_HKP \
  -o PFsnake/20261101_PF_HKP_out \
  -d /media/uhlemann/Core3_V2/REF/pf_ref.fasta \
  -p 2 \
  -K

Options

FlagDescription
-nDry-run
-KKeep-going
-p 1|2Single-end / paired-end mode
-cSnakemake cores

Expected Input

PFsnake/
|-- 20251101_PF_HKP/
|-- 20251101_PF_HKP_out/
|-- 20261101_PF_HKP/
|   |-- SAMPLE1_R1.fastq.gz
|   `-- SAMPLE1_R2.fastq.gz
`-- 20261101_PF_HKP_out/

pf_ref/
|-- pf_ref.fasta
`-- (optional annotation files)

Main Outputs

PFsnake/
|-- 20251101_PF_HKP/
|-- 20251101_PF_HKP_out/
|-- 20261101_PF_HKP/
`-- 20261101_PF_HKP_out/
    |-- 1_QC/
    |-- 2_bwa/
    |-- 3_bam_qc/
    |-- 4_gatk_out/
    |-- 6_cnv/
    |-- 7_mixed_infection/
    |-- 8_recomb_explore/
    `-- 9_drug_resistance/