bamtocov

bamtocov computes nucleotide coverage from sorted BAM or CRAM files to quantify read mapping across reference genomes for genomics analyses.

Key Features:

• Memory Efficiency: Implements a memory-efficient algorithm suitable for large-scale genomic data analysis.
• Stream Processing Capability: Reads sorted BAM or CRAM alignment files from streams to support integration into pipelines.
• Strand-Specific and Physical Coverage Analysis: Computes strand-specific (stranded) coverage and physical coverage metrics.
• Flexible Filtering Approaches: Provides filtering options to refine coverage calculations according to specified criteria.
• Multiple Output Formats: Exports coverage results in BED, Wig, or counts formats.

Scientific Applications:

• Nucleotide Coverage Quantification: Generates per-base coverage profiles for reference genomes to assess sequencing depth and completeness.
• RNA-seq Strand-Specific Analysis: Supports strand-specific coverage analysis to investigate read directionality and gene expression patterns in RNA-seq data.
• Downstream Coverage Mapping: Produces coverage maps for downstream analyses in genomic workflows, such as variant calling quality assessment and region-specific summary statistics.

Methodology:

Processes sorted BAM or CRAM files (including stream input) and computes coverage using a covtobed-based algorithm to generate coverage maps.