How ashwinth2k/bacterial-genome-pipeline works
This repository provides two implementations of a bacterial whole-genome variant-calling workflow: a linear Bash script and a config-driven Snakemake workflow. Both process reads through QC, trimming, alignment, post-alignment QC, variant calling/filtering, and QC reporting. The README documents the stages and required tools, but no source excerpts were available to verify finer-grained invocation or data wiring.
Main entry points: script.sh Variant calling · Snakefile Variant calling · config.yml Workflow config
Components 25
Bash workflow
- Bash pipeline
Bash/script.sh - Raw read QC
Bash/script.sh - Read trimming
Bash/script.sh - Read alignment
Bash/script.sh - Post-alignment QC
Bash/script.sh - Variant calling
Bash/script.sh - QC summary
Bash/script.sh
Snakemake workflow
- Snakemake pipeline
Snakemake/Snakefile - Raw read QC
Snakemake/Snakefile - Read trimming
Snakemake/Snakefile - Read alignment
Snakemake/Snakefile - Post-alignment QC
Snakemake/Snakefile - Variant calling
Snakemake/Snakefile - QC summary
Snakemake/Snakefile - Workflow config
Snakemake/config.yml
Analysis tools
- FastQC
- Trimmomatic
- BWA
- Samtools
- BCFtools
- MultiQC
Pipeline outputs
- Filtered variants
- QC report
Other components
- Raw reads
- E. coli reference
Connections 33
- Raw reads → Bash pipeline: input
- E. coli reference → Bash pipeline: reference
- Bash pipeline → Raw read QC: runs
- Raw read QC → Read trimming: then
- Read trimming → Read alignment: then
- Read alignment → Post-alignment QC: then
- Post-alignment QC → Variant calling: then
- Variant calling → QC summary: then
- Raw read QC → FastQC: uses
- Read trimming → Trimmomatic: uses
- Read alignment → BWA: uses
- Post-alignment QC → Samtools: uses
- Variant calling → BCFtools: uses
- QC summary → MultiQC: uses
- Variant calling → Filtered variants: produces
- QC summary → QC report: produces
- Raw reads → Snakemake pipeline: input
- E. coli reference → Snakemake pipeline: reference
- Workflow config → Snakemake pipeline: configures
- Snakemake pipeline → Raw read QC: runs
- Raw read QC → Read trimming: then
- Read trimming → Read alignment: then
- Read alignment → Post-alignment QC: then
- Post-alignment QC → Variant calling: then
- Variant calling → QC summary: then
- Raw read QC → FastQC: uses
- Read trimming → Trimmomatic: uses
- Read alignment → BWA: uses
- Post-alignment QC → Samtools: uses
- Variant calling → BCFtools: uses
- QC summary → MultiQC: uses
- Variant calling → Filtered variants: produces
- QC summary → QC report: produces