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
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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 |
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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 |
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SOAPdenovo | SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. | Latest Version: 1.04 |
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SOAPindel |
SOAPindel is developed to find the insertion and deletion specially for re-sequence technology. |
Coming soon. |
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SOAPsv | SOAPsv is a program for detecting the structural variation . | Coming soon. |
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SOAP v1 |
SOAP v1 is available all the same. |
Latest version: 1.11 |
Download
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SOAPaligner/soap2 | Version 2.20 For GNU Linux X86_64: |
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SOAPsnp | Version 1.03 |
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SOAPdenovo | Version 1.04 |
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Test Data | Version 20081210 |
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msort | Version 20081208 |
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Correction tool for SOAPdenovo | Version 20090703 |
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GapCloser for SOAPdenovo | Version 20100125 NEW |
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Discussion Group
We use Google Groups as SOAP's forum,news group and mailing list for the SOAP users.
BGI-SOAP
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Bug Report
Publications
♦ "SNP detection for massively parallel whole-genome resequencing" (2009) Genome Res. published online May 6, 2009 , doi:10.1101/gr.088013.108
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♦ "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
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Citation
♦ 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