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SOAPaligner specifications


Unique identifier OMICS_29049
Name SOAPaligner
Alternative names SOAP2, SOAP3, SOAP3-dp, SOAP3/GPU
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.21
Stability Stable
Maintained No




No version available


This tool is not available anymore.

Publications for SOAPaligner

SOAPaligner citations


Enhanced Fluorescent Siderophore Biosynthesis and Loss of Phenazine 1 Carboxamide in Phenotypic Variant of Pseudomonas chlororaphis HT66

Front Microbiol
PMCID: 5924801
PMID: 29740409
DOI: 10.3389/fmicb.2018.00759
call_split See protocol

[…] by SOAPdenovo V2.04 short sequence assembly software. Reads were compared with assembly Contig. According to the reads paired-end and overlap, the results were further optimized and assembled. Using SOAPaligner (version 2.21) sequence alignment software, all reads were mapped to the reference genome of P. chlororaphis HT66 (GenBank under the accession number ATBG00000000). The reads were trimmed […]


Whole Exome Sequencing Identified a Novel Heterozygous Mutation in HMBS Gene in a Chinese Patient With Acute Intermittent Porphyria With Rare Type of Mild Anemia

Front Genet
PMCID: 5920022
PMID: 29731767
DOI: 10.3389/fgene.2018.00129
call_split See protocol

[…] gn clean reads to the human reference genome (hg19) with maximum 3 mismatches, the parameters were set as ‘-a -b -D -o -u -2 -t -v 3 -l 35 -s 40 -m 0 -x 500 -p 4 -r 1 -n 0’. Based on the results from SOAPaligner, software SOAPsnp (v1.05) was used to assemble the consensus sequence and call genotypes in target regions. The following parameters were set: -Q k -i -d -o -r 0.0005 -e 0.001 -u -L 90 -T […]


Impact of Three Different Mutations in Ehrlichia chaffeensis in Altering the Global Gene Expression Patterns

Sci Rep
PMCID: 5906474
PMID: 29670161
DOI: 10.1038/s41598-018-24471-3

[…] n filtered to remove adapter sequences and low quality reads, then clean reads were aligned to the E. chaffeensis Arkansas strain complete genome as per the first annotated GenBank # CP000236.1 using SOAPaligner/SOAP2. We opted to use this accession number because our prior publications, and similarly other investigators, widely used it for referring to gene names and numbers listed in it. Not mor […]


Identification of Major Rhizobacterial Taxa Affected by a Glyphosate Tolerant Soybean Line via Shotgun Metagenomic Approach

PMCID: 5924556
PMID: 29659545
DOI: 10.3390/genes9040214

[…] , and C). On the other hand, Rahnella in the MGNRh sample had only 510 mapped reads, which was only 0.00834% of the total mapped clean reads (, ). Both results were consistent with those analyzed by SOAPaligner and revealed by 16S rDNA V5–V7 amplicon deep sequencing (A,C). Serratia was also discovered in the MGMRh sample, but it was detected with much less mapped reads in the MGNRh sample. Meanwh […]


Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China

Sci Rep
PMCID: 5883011
PMID: 29615795
DOI: 10.1038/s41598-018-23986-z

[…] utput was divided into single-tag data sets using a Perl script, and then the single tags with restriction site were extracted. These tags of each individual were mapped to the reference genome using SOAP2 program ( with the parameter −M 4, −v 2 and −r 0 allowing four mismatches. The sequences that aligned with only one location were regarded as unique tags and the exp […]


Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

BMC Genomics
PMCID: 5863803
PMID: 29566661
DOI: 10.1186/s12864-018-4609-x
call_split See protocol

[…] value of < 5%) were removed after data filtering. After data filtering, in average, ∼ 95% clean reads remained in each sample. Clean reads were then mapped to the genome of A. nidulans (AspGD) using SOAPALIGNER/SOAP2 []. In the alignment, no more than two mismatches were allowed. On average, 90% total mapped reads to the genome was achieved. The gene expression level was calculated by using FPKM […]


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SOAPaligner institution(s)
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China; School of Computer Science, National University of Defense Technology, Changsha, China; BGI-Shenzhen, Shenzhen, Guangdong, China; Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA
SOAPaligner funding source(s)
Supported by General Research Fund 10612042, by Hong Kong ITF Grant GHP/011/12 and by the GRF Grant HKU-713512E.

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