SOAPsnp

SOAPsnp constructs accurate consensus sequences and detects single nucleotide polymorphisms (SNPs) from next-generation sequencing alignment outputs for resequencing analyses.

Key Features:

• Consensus Sequence Building: Processes alignment outputs from soap1 and SOAPaligner/soap2 to generate high-quality consensus sequences, optimized for sequencing-by-synthesis platforms such as the Illumina Genome Analyzer and for assembling nonrepetitive regions across diploid autosomes and haploid chromosomes.
• SNP Detection: Identifies SNPs from whole-genome or targeted resequencing and assigns a per-base quality score derived from Bayesian theory to assess consensus-calling accuracy.
• Quality and Accuracy: Integrates data quality metrics, alignment considerations, and common experimental errors into consensus calling and demonstrated high concordance with Illumina Human 1M BeadChip genotypes on 36x human resequencing data (98.6% concordance on X chromosome and 98% on autosomes).
• Coverage and False Call Rate: Provides extensive genome coverage at high sequencing depths with low false call rates and uses prior allele probabilities from dbSNP to improve detection of known SNPs at lower depths.

Scientific Applications:

• Genetic Variation Studies: Enables accurate resequencing of whole genomes or specific regions to characterize genetic diversity.
• Disease Research: Facilitates identification of SNPs and reliable consensus sequences to support studies of genetic contributors to disease.
• Population Genetics: Supports population-level analyses of genetic variation relevant to evolutionary and epidemiological research.

Methodology:

SOAPsnp uses alignment outputs from soap1 and SOAPaligner/soap2 and applies a Bayesian model to combine sequencing quality metrics, alignment information, and experimental-error considerations into per-base quality scores while optionally incorporating prior allele probabilities from dbSNP.