SHORTY

SHORTY assembles short paired-end sequencing reads (25–30 bases) from next-generation platforms such as ABI SOLiD into contiguous sequences for de novo genome reconstruction.

Key Features:

• Seed-Based Assembly Approach: Employs 5–10 seed sequences of 300–500 bp to anchor assembly and enable construction of assemblies from short reads at up to 100x coverage.
• Single Seed Reads Utilization: Uses single seed reads to stabilize and crystallize assemblies derived from short-read data.
• Accurate Intercontig Distance Estimation: Estimates intercontig distances using multiple spanning paired-end reads to resolve genomic regions.

Scientific Applications:

• Bacterial Genome Assembly: Assembles bacterial genomes, achieving N50 contig sizes of approximately 40 kb on simulated SOLiD data.
• Comparative Performance: On simulated data SHORTY's results surpass those of competing assemblers, while real-data performance can be limited by sequencing artifacts.

Methodology:

Augments short paired reads with 5–10 seeds (300–500 bp), leverages single seed reads to anchor assemblies, and estimates intercontig distances from multiple spanning paired-end reads.