SOAPdenovo v2.04 (with source code) NEW is released ; (See Download)
SOAPaligner-v2.21 NEW is released under GNU GPL v3. (See Download)

Introduction

SOAP has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis. Currently, it consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ) and a de novo short reads assembler ( SOAPdenovo ). And a GPU-accelerated alignment tool (SOAP3/GPU) are being implemented.

Software

SOAPdenovo NEW SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. Latest Version: 2.04
SOAP3/GPU SOAP3 is a GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3. When compared with its previous version SOAP2, SOAP3 can be up to tens of times faster. Latest Version: 0.01 beta
SOAPaligner/soap2 SOAPaligner/soap2 is a program for faster and efficient alignment for short oligonucleotide onto reference sequences. SOAPaligner/soap2 is compatible with numerous applications, including single-read or pair-end resequencing. Latest Version: 2.20
SOAPsplice NEW
SOAPsplice is designed to use RNA-Seq reads for genome-wide ab initio detection of splice junction sites and identification of alternative splicing (AS) events.
Latest Version: 1.1
SOAPsnp
SOAPsnp is an accurate consensus sequence builder based on soap1 and SOAPaligner/soap2's alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs.

Latest Version: 1.03
SOAPindel
SOAPindel is developed to find the insertion and deletion specially for re-sequence technology.

Latest Version: 1.0
SOAPsv SOAPsv is a program for detecting the structural variation . Latest Version: 1.02
SOAP v1
SOAP v1 is available all the same.

Latest version: 1.11

Download

SOAPdenovo(with source code) Version 2.04 NEW Download
Correction tool for SOAPdenovo Version v2.01 NEW Download
GapCloser for SOAPdenovo Version v1.12 NEW Download
SOAP3/GPU Version 0.01 betaNEW Download
SOAPaligner/soap2 Version 2.21 for GNU Linux X86_64NEW Download
SOAPaligner/soap2 Version 2.20 for GNU Linux X86_64
Source version with index builder.NEW (Under GNU GPL v3)
Download
Download
SOAPsplice Version 1.0 NEW Download
SOAPsnp Version 1.03 Download
Test Data Version 20081210 Download
msort Version 20130809 Download
soap.coverage Version 2.7.7 Download
soap2sam Version 0.1.1 Download


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Discussion Group

We use Google Groups as SOAP's forum,news group and mailing list for the SOAP users.

Google Groups          BGI-SOAP
 
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Bug Report

 
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Publications

Luo et al.: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012 1:18. Download PDF

Li et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2010) vol. 20 (2) pp. 265-72 Download PDF

"SNP detection for massively parallel whole-genome resequencing" (2009) Genome Res. published online May 6, 2009 , doi:10.1101/gr.088013.108 Download PDF

"SOAP2: an improved ultrafast tool for short read alignment" (2009) BIOINFORMATICS, doi:10.1093/bioinformatics/btp336   See on Oxford Journals website

"SOAP: short oligonucleotide alignment program" (2008) BIOINFORMATICS,Vol. 24 no.5 2008, pages 713–714 doi:10.1093/bioinformatics/btn025   Download PDF

Citation   
♦ To reference the SOAPdenovo, please cite this paper:
Luo et al.: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012 1:18.

♦ To reference the SOAPsnp, please cite this paper :
Ruiqiang Li, Yingrui Li, Xiaodong Fang, et al. (2009) "SNP detection for massively parallel whole-genome resequencing" (2009) Genome Res. , doi:10.1101/gr.088013.108

♦ To reference the SOAP 2, please cite this paper :
Li et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. BIOINFORMATICS, doi:10.1093/bioinformatics/btp336

♦ To reference the SOAP v1 program, please cite this paper :
Li et al. (2008) SOAP: short oligonucleotide alignment program" . BIOINFORMATICS, 24 no.5,713–714, doi:10.1093/bioinformatics/btn025


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