inGAP

inGAP detects and evaluates single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (indels) from next-generation sequencing data by comparing high-throughput pyrosequencing reads to reference genomes from related organisms.

Key Features:

• Versatile Read Handling: inGAP processes sequencing data from Roche/454, Illumina, and Sanger platforms without restriction on read length.
• Bayesian variant detection: Employs a Bayesian algorithmic framework to compute probabilities for SNP and indel calls.
• Reference-based comparison: Compares high-throughput pyrosequencing reads against reference genomes from related organisms.
• High accuracy: Experimental validation reports approximately 97% accuracy for SNP detection and 94% accuracy for indel detection.
• Comparative genomics: Supports comparison of multiple genomes for analyses of conservation and divergence.
• Bacterial genome assembly support: Provides functionality to assist bacterial genome assembly.

Scientific Applications:

• Genetic variation studies: Detection of SNPs and indels to investigate genetic diversity, identify disease-associated mutations, and infer evolutionary relationships.
• Microbial genomics: Bacterial genome assembly and variation analysis for studies of microbial genetics, pathogen evolution, and antibiotic resistance mechanisms.
• Comparative genomics: Multiple-genome comparisons to assess genomic conservation and divergence among species or within populations.

Methodology:

inGAP applies a Bayesian algorithmic framework to compare high-throughput pyrosequencing and other reads (Roche/454, Illumina, Sanger) against reference genomes and compute probabilities for SNP and indel detection.