Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 25 (15), 1966-7

SOAP2: An Improved Ultrafast Tool for Short Read Alignment

Affiliations

SOAP2: An Improved Ultrafast Tool for Short Read Alignment

Ruiqiang Li et al. Bioinformatics.

Abstract

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.

Similar articles

  • Short Read Alignment Using SOAP2
    B Hurgobin. Methods Mol Biol 1374, 241-52. PMID 26519410.
    Next-generation sequencing (NGS) technologies have rapidly evolved in the last 5 years, leading to the generation of millions of short reads in a single run. Consequently …
  • Ψ-RA: A Parallel Sparse Index for Genomic Read Alignment
    M Oğuzhan Külekci et al. BMC Genomics 12 Suppl 2 (Suppl 2), S7. PMID 21989248.
    Ψ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology. Ψ-RA is very fast in …
  • CUSHAW: A CUDA Compatible Short Read Aligner to Large Genomes Based on the Burrows-Wheeler Transform
    Y Liu et al. Bioinformatics 28 (14), 1830-7. PMID 22576173.
    We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphi …
  • A Survey of Sequence Alignment Algorithms for Next-Generation Sequencing
    H Li et al. Brief Bioinform 11 (5), 473-83. PMID 20460430. - Review
    Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence r …
  • Gene Prediction: Compare and CONTRAST
    P Flicek. Genome Biol 8 (12), 233. PMID 18096089. - Review
    CONTRAST, a new gene-prediction algorithm that uses sophisticated machine-learning techniques, has pushed de novo prediction accuracy to new heights, and has significantl …
See all similar articles

Cited by 1,423 PubMed Central articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback