Shore

Shore analyzes short-read sequencing data to detect single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and regions of genomic divergence relative to a reference for comparative and polymorphism studies.

Key Features:

• Polymorphism Detection: Identifies SNPs and 1- to 3-bp indels with high specificity (>99%), detecting 823,325 unique SNPs and 79,961 unique 1- to 3-bp indels in three Arabidopsis thaliana accessions (Col-0, Bur-0, Tsu-1).
• Error Identification: Detects potential errors in reference genome sequences, reporting over 2,000 potential errors in the Col-0 reference.
• Genomic Variation Analysis: Identifies regions that are extremely dissimilar, deleted, or duplicated relative to a reference, detecting more than 3.4 Mb of such variation in Bur-0 and Tsu-1 versus Col-0.
• De Novo Assembly Integration: Incorporates targeted de novo assembly using the Velvet assembler to generate 10,921 high-confidence contigs anchored to flanking sequences and resolving indels up to 641 bp.
• Broad Applicability: Applies across moderate to large genomes, including highly diverged loci, and supports estimation of necessary sequencing coverage depth for functional and evolutionary studies.

Scientific Applications:

• Comparative Genomics / Whole-Genome Hybridization: Supports comparative analyses and whole-genome hybridization studies, as exemplified by analyses in the 1001 Genomes Project for Arabidopsis thaliana.
• Genetic Diversity and Evolutionary Biology: Enables analysis of intra-species genetic diversity and evolutionary relationships through accurate SNP, indel, and structural-variation detection.
• Functional Genomics: Facilitates functional-genomics investigations by providing variant calls and assembled contigs for highly diverged genomic loci.

Methodology:

Aligns short reads and predicts SNPs and indels, and performs targeted de novo assembly with the Velvet assembler, anchoring assembled contigs to flanking sequences.