SOAP2

SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide
alignment program that both reduces computer memory usage and increases alignment
speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT)
compression index to substitute the seed strategy for indexing the reference
sequence in the main memory. We tested it on the whole human genome and found
that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved
alignment speed by 20-30 times. SOAP2 is compatible with both single- and
paired-end reads. Additionally, this tool now supports multiple text and
compressed file formats. A consensus builder has also been developed for
consensus assembly and SNP detection from alignment of short reads on a reference
genome. AVAILABILITY: http://soap.genomics.org.cn.

SOAP2: an improved ultrafast tool for short read alignment.

SOAP2 is a software tool for quickly and accurately aligning short reads to a reference sequence. It utilizes a Burrows-Wheeler Transformation (BWT) compression index to replace the seed strategy of indexing the reference sequence in main memory, resulting in 5.4 GB of memory usage and a 20-30x speed improvement over prior versions. It supports single- and paired-end reads and various text and compressed file formats. A consensus builder is also included for consensus assembly and SNP detection.

SOAP2

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