SOAP :: Short Oligonucleotide Analysis Package

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:
	SOAPsnp	Version 1.03 ^NEW
	SOAPdenovo	Version 1.03 ^NEW
	Test Data	Version 20081210

Discussion Group

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

BGI-SOAP

Bug Report

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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