SOAP2

SOAP2 aligns short oligonucleotide sequences to reference genomes for rapid, memory-efficient short-read mapping and downstream consensus assembly and SNP detection.

Key Features:

• Burrows-Wheeler Transformation (BWT) index: Uses a BWT compression index to index reference sequences directly in main memory, replacing traditional seed strategies.
• Memory efficiency: Reduces memory usage from 14.7 GB to 5.4 GB when applied to the entire human genome.
• Speed: Enhances alignment speed by approximately 20-30 times compared with its predecessor.
• Read types supported: Supports both single-read and paired-end resequencing applications.
• File format support: Accommodates multiple text and compressed file formats.
• Consensus builder: Integrates a consensus builder that facilitates consensus assembly and SNP detection from aligned short reads on reference genomes.
• Benchmarking: Has been compared in benchmarking studies with Bowtie, BWA, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST.

Scientific Applications:

• Short-read mapping: Alignment of short oligonucleotide sequences generated by next-generation sequencing to reference genomes.
• Resequencing studies: Single-read and paired-end resequencing for variant discovery and genome analysis.
• SNP detection and consensus assembly: Generation of consensus sequences and identification of single nucleotide polymorphisms from aligned reads.

Methodology:

SOAP2 employs a Burrows-Wheeler Transformation (BWT) compression index to index reference sequences in main memory instead of seed-based indexing and includes a consensus builder for consensus assembly and SNP detection from aligned short reads.