sv-gen

sv-gen generates artificial short-read alignments with and without structural variants from a reference genome using a Snakemake-based workflow.

Key Features:

• Snakemake-based workflow: Orchestrates analysis steps using a Snakemake workflow engine.
• Parallel processing: Supports parallel execution to handle large datasets efficiently.
• Portability: Runs on Linux-based environments.
• Scalability: Scales from single-node to multi-node high-performance computing environments.
• Extensibility: Allows addition of new analysis tools into the workflow.
• SURVIVOR: Integrates SURVIVOR for merging structural variant calls from multiple callers.
• ART: Uses ART for generating synthetic short reads with or without structural variants.
• BWA: Employs BWA for mapping short reads to a reference genome.
• Samtools: Uses Samtools to manipulate and query SAM/BAM alignment files.

Scientific Applications:

• Artificial genome generation with structural variants: Produces artificial genomes and corresponding short-read alignments containing structural variants from a reference genome.
• Short-read sequencing simulation: Generates simulated short-read sequencing data with or without structural variants using ART.
• Structural variant call integration: Merges structural variant calls from multiple callers using SURVIVOR for downstream analysis.
• Alignment generation and processing: Generates mapped short-read alignments with BWA and processes alignments in SAM/BAM format with Samtools.

Methodology:

Snakemake-based workflow that incorporates ART, BWA, Samtools, and SURVIVOR and supports parallel execution on Linux and HPC environments.