SOAP :: Short Oligonucleotide Analysis Package

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

Discussion Group

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

BGI-SOAP

Bug Report

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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