SOAP protocols

SOAP specifications

Information


Unique identifier OMICS_00688
Name SOAP
Alternative name Short Oligonucleotide Analysis Package
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format Tab-delimited text, SAM
Operating system Unix/Linux
Programming languages C++, Perl
Parallelization CUDA
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Short_Oligonucleotide_Analysis_Package

Subtool


  • GapCloser

Download


Versioning


Add your version

Maintainers


  • person_outline SOAP3 <>
  • person_outline Tak-Wah Lam <>
  • person_outline Yingrui Li <>
  • person_outline Ruiqiang Li <>

Publication for Short Oligonucleotide Analysis Package

SOAP IN pipelines

 (15)
2018
PMCID: 5892942
PMID: 29570727
DOI: 10.1371/journal.ppat.1006942

[…] checked by fastqc [54]. mirtools2.0 [55] pipeline is used for trimming (“adaptor_trim.pl” script) and downstream analysis of known mirnas. sequencing reads are aligned to the bostau7 genome using soap [56]. annotations are added from mirbase 21 [57] and rfam [58] databases. the differential expression of each known mirnas from their absolute read counts are analysed by deseq2 [34]. […]

2017
PMCID: 5660214
PMID: 29079830
DOI: 10.1038/s41598-017-14738-6

[…] from ncbi (srr555564)33 and assembled into unigenes using the trinity 2.4.0 software48. the snp-associated rad tag sequences were aligned against the assembled transcriptome of a. konjac using soap 2.2149 with the default settings. to investigate the gene function of loci, a blastx search was applied against ncbi’s non-redundant database by blast 2.2.2850 with an e-value of 1e−6. according […]

2016
PMCID: 5084872
PMID: 27789648
DOI: 10.1128/genomeA.01218-16

[…] reactions were performed according to the manufacturer’s instructions and a 300 pair-end library was generated. the resulting sequences were de novo assembled using soapdenovo v2.01 (http://soap.genomics.org.cn/) (6). for the prokaryotic organism, we used an ab initio prediction method to get gene models for strain av208. gene models were identified using glimmer 3 (7). then, all gene […]

2015
PMCID: 4686875
PMID: 26690086
DOI: 10.1038/srep18470

[…] with poly (a) or simple repeats, and (6) reads shorter than 18 nt. the clean reads were screened against and mapped to the latest ovine genome assembly (oar_v3.1, released sept. 20, 2012) using the soap program (soap aligner v2.21, http://soap.genomics.org.cn/)37. after mapping, we used the clc genomics workbench 5.5 tool to blast the clean reads against the rfam database […]

2015
PMCID: 4686875
PMID: 26690086
DOI: 10.1038/srep18470

[…] or simple repeats, and (6) reads shorter than 18 nt. the clean reads were screened against and mapped to the latest ovine genome assembly (oar_v3.1, released sept. 20, 2012) using the soap program (soap aligner v2.21, http://soap.genomics.org.cn/)37. after mapping, we used the clc genomics workbench 5.5 tool to blast the clean reads against the rfam database […]

SOAP institution(s)
Beijing Genomics Institute at Shenzhen, Shenzhen, China; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
SOAP funding source(s)
Supported by the National Natural Science Foundation of China (30725008), and grants from the Danish Natural Science Research Council (272-05- 0344 and 272-07-0196).

SOAP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SOAP