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SSIAMB

Welcome to the SSIAMB documentation!

SSIAMB (SSI Ambiguous Site Detection Tool) is a bioinformatics tool for detecting and analyzing ambiguous sites in bacterial genomic sequences.

Overview

SSIAMB provides comprehensive analysis of ambiguous sites in genomic data by:

  • Processing BAM alignment files to identify ambiguous sites
  • Calculating depth and quality metrics
  • Generating detailed reports and summaries
  • Supporting multiple alignment and variant calling workflows

Quick Start

Installation

pip install ssiamb

Basic Usage

# Analyze a BAM file for ambiguous sites
ssiamb analyze sample.bam --reference ref.fasta --output results/

# Process with custom thresholds
ssiamb analyze sample.bam --reference ref.fasta --min-depth 10 --min-quality 20

Features

  • Multi-format support: Works with BAM alignment files
  • Flexible workflows: Compatible with BWA and Minimap2 aligners
  • Quality control: Comprehensive depth and quality filtering
  • Rich output: Detailed reports and summary statistics
  • Galaxy integration: Available as a Galaxy tool

Documentation Structure

Support