Illumina WGS

shortWGS

QC, Kraken2 species inference, SRST2 typing, TETyper, and HTML/CSV summary generation.

Pipeline Flow

Prefilter→ fastp→ Kraken2→ SRST2 (MLST/ARG/Plasmid)→ TETyper→ MultiQC + Summary

Build

cd shortWGS
docker build --network=host -t shortwgs:1.0 .

Run

./shortWGS/Go_shortWGS.sh \
  -i /path/to/fastq \
  -o /path/to/output \
  -d /path/to/WGS_DB2 \
  -k /path/to/kraken2_db \
  -r /path/to/GoWGS \
  -K

Real Example

Go_shortWGS.sh \
  -i shortWGS/20261101_WGS_HKP \
  -o shortWGS/20261101_WGS_HKP_out \
  -d /media/uhlemann/core4/DB/WGS_DB2 \
  -k /media/uhlemann/core4/DB/kraken2DB/k2_pluspfp_16gb_20241228 \
  -r /home/uhlemann/heekuk_path/GoWGS \
  -K

Options

Flag	Description
`-n`	Dry-run
`-K`	Keep-going
`-c`	Snakemake cores
`-m`	Custom docker image tag

Expected Input

shortWGS/
|-- 20251101_WGS_HKP/
|-- 20251101_WGS_HKP_out/
|-- 20261101_WGS_HKP/
|   |-- SAMPLE1_R1.fastq.gz
|   `-- SAMPLE1_R2.fastq.gz
`-- 20261101_WGS_HKP_out/

WGS_DB2/
|-- CARD/
|-- PlasmidFinder/
|-- MLST/
`-- tetyper/

kraken2_db/
`-- (kraken2 index files)

GoWGS/
`-- scripts/
    `-- 20251007_Summary_WGS_tem_v3.Rmd

Main Outputs

shortWGS/
|-- 20251101_WGS_HKP/
|-- 20251101_WGS_HKP_out/
|-- 20261101_WGS_HKP/
`-- 20261101_WGS_HKP_out/
    |-- 1_fastp_out/
    |-- 2a_kraken2/
    |-- 2_ST_srst2_out/
    |-- 3_ARGs_srst2_out/
    |-- 4_Plasmid_srst2_out/
    |-- 5_TETyper/
    |-- multiqc_report.html
    |-- summary_master.csv
    `-- summary_report.html   <-- FINAL REPORT FILE