SOAP

SOAP aligns short oligonucleotides to reference sequences for analysis of high-throughput next-generation sequencing data, including reads from Illumina-Solexa platforms.

Key Features:

• Gapped and Ungapped Alignment: Performs both gapped and ungapped alignments for short oligonucleotides.
• Compatibility with NGS Data: Optimized for large datasets produced by next-generation sequencing technologies including Illumina-Solexa.
• Multi-threaded Parallel Computing: Supports multi-threaded parallel computing to process multiple query sets concurrently.
• Batch Processing Module: Enables batch processing of multiple query sets for efficient management of large datasets.
• Supported Applications: Compatible with single-read and paired-end resequencing, small RNA discovery, and mRNA tag sequence mapping.
• SOAP3-dp CPU/GPU Optimization: SOAP3-dp leverages CPU and GPU optimized algorithms to increase speed and sensitivity compared with other aligners (BWA, Bowtie2, SeqAlto, CUSHAW2, GEM, BarraCUDA, CUSHAW).
• Gapped Alignment Sensitivity: SOAP3-dp supports gapped alignments down to ~60% similarity, facilitating detection of longer insertions and deletions (Indels) and more authentic variants.
• BAM Support and Scoring: SOAP3-dp natively supports the BAM file format and uses the same scoring scheme as BWA.
• Performance and Evaluation: Reported to be two to ten times faster while maintaining high sensitivity and low false discovery rate (FDR) on Illumina reads of varying lengths.
• Real-data Validation: Evaluations on human genome data and fosmid sequencing demonstrated increased authentic variant discovery and a 9.1% FDR on newly discovered deletions.

Scientific Applications:

• Resequencing: Single-read and paired-end resequencing for genetic variant discovery.
• Small RNA Discovery: Detection and mapping of small RNAs from high-throughput sequencing data.
• mRNA Tag Mapping: Mapping of mRNA tag sequences to reference genomes.
• Variant and Indel Detection: Identification of genetic variants and longer insertions/deletions enabled by gapped alignment sensitivity.

Methodology:

Performs gapped and ungapped alignments; supports multi-threaded parallel computing; SOAP3-dp implements CPU- and GPU-optimized algorithms, native BAM support, and the BWA scoring scheme; evaluated on Illumina reads, human genome data, and fosmid sequencing with comparative performance analyses against BWA, Bowtie2, SeqAlto, CUSHAW2, GEM, BarraCUDA, and CUSHAW.