SHRiMP

SHRiMP maps short next-generation sequencing reads to reference genomes to enable detection of genetic variation in highly polymorphic and non-model species.

Key Features:

• Short-read support: Supports mapping of short reads (25-70 bp) typical of next-generation sequencing.
• Polymorphism-aware mapping: Maps reads accurately to targets with significant polymorphism to facilitate analysis of genetic variation.
• Data representation compatibility: Handles letterspace (e.g., Roche, Illumina), colourspace (Applied Biosystems AB SOLiD), and Helicos space representations.
• Fast mapping technique: Implements a rapid read mapping approach to improve throughput for large datasets.
• Alignment methods by encoding: Provides distinct alignment methods tailored for letter-space and AB SOLiD (color-space) reads.
• Statistical model for false positives: Integrates a statistical model to reduce false positive mapping hits.

Scientific Applications:

• Population genomics of non-model species: Enables analysis of genetic diversity and polymorphism in non-model organisms using short-read data.
• Ciona savignyi heterozygosity assessment: Has been applied to map reads from a newly sequenced Ciona savignyi individual to its reference genome to assess high heterozygosity.

Methodology:

Implements a rapid read mapping technique, distinct alignment methods for letter-space and AB SOLiD (color-space) reads, and a statistical model to minimize false positive hits while handling letterspace, colourspace, and Helicos space representations for short reads (25-70 bp).