SHARCGS

SHARCGS assembles short-read high-throughput sequencing data de novo to produce accurate contigs for genomic analysis.

Key Features:

• High Throughput Capability: Optimized for large datasets from next-generation sequencing technologies and capable of producing gigabase-scale assemblies.
• Short-Read Assembly: Specifically addresses assembly of short reads (25–40-mers), including outputs from Illumina's 1G sequencer.
• Accuracy and Speed: Demonstrates superior speed and accuracy relative to existing assembly algorithms.
• Robustness Against Errors: Manages missing reads and incorrect base calls to produce high-quality assemblies under suboptimal conditions.

Scientific Applications:

• Eukaryotic Genomes: Tested on BAC inserts from Drosophila and Arabidopsis, achieving simulated N50 sizes greater than 20 kbp in datasets that include data imperfections.
• Yeast Chromosomes: Demonstrated efficacy in assembling yeast chromosomes.
• Bacterial Genomes: Applied to bacterial genomes including Haemophilus influenzae and Escherichia coli.

Methodology:

Assembles short-read data into contigs; produced 949,974 contigs longer than 50 bp with nearly all aligning error-free to references, and assembled 36-mer reads for Helicobacter acinonychis covering 98% of the genome with an N50 of 3.7 kbp and minimal discrepancies.