AlignmentAndQCWorkflows
AlignmentAndQCWorkflows provides Roddy-based workflows for alignment and quality control of next-generation sequencing data. The plug-in includes workflows for whole-genome sequencing, whole-exome sequencing, and whole-genome bisulfite sequencing that are based on BWA MEM alignments. The workflows include extensive quality control steps for BAM files, using parallelized piping into multiple QC tools to improve performance.
Key benefits
Provides Roddy-compatible workflows for NGS alignment and quality control
Supports WGS, WES, and WGBS data processing
Includes PanCancer alignment workflows for genome and exome data
Provides a bisulfite core workflow using methylCtools
Optimized BAM-level quality control through high-performance I/O minimizing processing
Applications
Alignment of whole-genome and targeted sequencing data, such as whole-exome sequencing
Processing of whole-genome bisulfite sequencing datasets
Quality control of aligned BAM files
Analysis of individual samples or tumor–control sample combinations
Integration into Roddy-based standardized NGS processing pipelines
Stand-alone and or as alignment workflow for the One-Touch-Pipeline (OTP) workflow automation management platform
Intended use
AlignmentAndQCWorkflows is intended for bioinformaticians, genomics researchers, sequencing facilities, and infrastructure teams working with human NGS datasets. It is particularly suited for users who need performant, standardized, and BWA-based alignments, BAM-level quality control, and processing of WGS, WES, or WGBS data in reproducible analysis environments.
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