Alignment Quality Control

About

Streamlines the preliminary assessment of genomic alignment files by generating comprehensive technical metrics using industry-standard tools like samtools, Picard, and MultiQC. It automates the process of checking read depth, mapping quality, error rates, and insert size distributions while ensuring BAM files are correctly formatted, sorted, and indexed. This skill is essential for bioinformaticians needing to validate data quality and prepare datasets for peak calling or open chromatin analysis without manually orchestrating complex command-line sequences.

Key Features

• Automated BAM formatting, sorting, and read group validation
• Consolidated MultiQC visual reports and PASS/WARN/FAIL summary tables
• PCR duplication rate estimation and mitochondrial contamination analysis
• 2 GitHub stars
• Comprehensive mapping statistics including read depth and quality metrics
• Fragment length profile generation via insert size distribution metrics

Use Cases

• Assessing aligner performance and mapping efficiency for sequencing runs
• Validating BAM file formatting and sorting prior to secondary processing
• Generating standardized quality reports for ChIP-seq or ATAC-seq datasets