SHE-RA

SHE-RA converts short-read sequencing data into longer, high-quality composite reads by joining overlapping mate-pair sequences to approximate Sanger sequencing accuracy for applications that require extended read length.

Key Features:

• Composite Read Generation: Constructs longer composite reads from short-read sequences by leveraging overlapping mate-pair sequences to extend read lengths beyond 200 base pairs while maintaining quality scores comparable to Sanger sequencing.
• Automatable Library Construction: Incorporates an automatable, gel-less library construction step that produces appropriately sized inserts to generate overlapping mate-pair sequences.
• Paired-End Sequencing Compatibility: Operates with paired-end sequencing on short-read instruments, enabling alignment of mate-pair reads and joining of overlapping segments into longer composite reads.

Scientific Applications:

• Metagenomic analyses: Provides longer composite reads at reduced cost to improve taxonomic and functional profiling in metagenomic studies.
• Genomic studies on short-read platforms: Facilitates comprehensive genomic analyses using platforms such as the Illumina Genome Analyzer by offering low error rates and lower cost compared to pyrosequencing.

Methodology:

The pipeline begins with automatable, gel-less library construction to generate appropriately sized inserts, proceeds through paired-end sequencing on short-read instruments, and performs strategic joining of overlapping mate-pair sequences to create longer composite reads.