SAMStat

SAMStat analyzes sequence alignment/map (SAM) files to extract and summarize nucleotide- and alignment-related statistics for detection of biases that affect mapping rate and accuracy.

Key Features:

• Nucleotide Overrepresentation Analysis: Provides plots and summaries of nucleotide overrepresentation in both mapped and unmapped reads to reveal sequence-specific errors or biases.
• Comprehensive Alignment Statistics: Computes a range of alignment metrics from SAM files, including mapping rates and alignment characteristics derived from short-read alignments against a reference genome.
• Bias Identification to Inform Filtering: Analyzes sequence features within mapped data to identify protocol-specific biases and inform downstream decisions such as read trimming or filtering.
• Efficient C implementation: Implemented as an efficient C program for processing large SAM-format datasets.

Scientific Applications:

• Alignment quality assessment: Detects nucleotide- and alignment-related issues that can reduce mapping accuracy and inform quality-control measures.
• Protocol bias evaluation: Identifies biases introduced by sequencing or sample-preparation protocols to guide experimental design adjustments.
• Longitudinal data quality tracking: Provides summary statistics useful for monitoring sequencing data quality over time in large-scale projects.

Methodology:

Parses SAM format files to extract nucleotide distributions and alignment characteristics from mapped and unmapped reads, computes summary statistics, and generates visual representations that highlight potential biases or errors.