BAM Filtration

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Streamlines the preprocessing of sequencing data by automating the removal of technical artifacts from BAM files, such as unmapped reads and genomic blacklisted regions. Designed specifically for ChIP-seq and ATAC-seq workflows, it ensures data integrity through coordinate-sorting checks and read group validation before generating high-quality filtered outputs. This automated pipeline acts as an essential bridge between raw alignment and downstream analysis, helping researchers maintain a clean and reproducible bioinformatics environment while handling complex directory structures and tool dependencies.

Características Principales

• Automated removal of mitochondrial reads, PCR duplicates, and unmapped reads
• Interactive prompting for missing configuration files and blacklist paths
• Integration with genomic blacklist BED files for region-specific filtering
• Validation of coordinate-sorted BAMs and Read Group (RG) information
• Standardized project directory initialization and output management
• 2 GitHub stars

Casos de Uso

• Preprocessing ChIP-seq or ATAC-seq data before peak calling
• Cleaning artifacts and 'bad reads' from sequencing datasets
• Standardizing genomic data filtration workflows for reproducible research