The Latest News:    SOAPdenovo (v1.03) is released.(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 ).

Software

SOAPaligner/soap2 SOAPaligner/soap2 is a program for faster and efficient alignemt for short oligonucleotide onto reference sequences. SOAPaligner/soap2 is compatible with numerous applications, including single-read or pair-end resequencing. Latest Version: 2.18
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
SOAPdenovo SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. Latest Version: 1.03
SOAPindel
SOAPindel is developed to find the insertion and deletion specially for re-sequence technology.

Coming soon.
SOAPsv SOAPsv is a program for detecting the structural variation . Coming soon.
SOAP v1
SOAP v1 is available all the same.

Latest version: 1.11

Download

SOAPaligner/soap2 Version 2.18
For GNU Linux X86_64:

Download
SOAPsnp Version 1.03 NEW Download
SOAPdenovo Version 1.03 NEW Download
Test Data Version 20081210 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
 
E-mail:
Access to "BGI-SOAP" group
 

Bug Report

 
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Publications

"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 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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