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novoSNP specifications

Information


Unique identifier OMICS_10354
Name novoSNP
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data novoSNP takes a reference sequence and a number of sequencing trace files as input.
Output data It generates a list of possible variations with a quality score.
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for novoSNP

novoSNP in publications

 (36)
PMCID: 5852028
PMID: 29540704
DOI: 10.1038/s41598-018-22337-2

[…] sanger sequencing, including amplification, sequencing, and analysis of the target fragments, have been previously described. sequence alignment and analysis of variations were performed by using the novosnp program.table 3note: pcr conditions: 35 cycles of amplification. each cycle consists of 30 s denaturation at 94 °c, 60 s annealing ranging from 59.5 °c to 60.9 °c and 1 min extension at 72 °c, […]

PMCID: 5796065
PMID: 29301249
DOI: 10.3390/ijms19010116

[…] uv light, recovered using genejet gel extraction and dna cleanup micro kit (thermo fisher scientific), and used for sanger sequencing (genscript, piscataway, nj, usa)., snps were identified using novosnp program [], which could detect heterozygous sequence data based on a cumulative scoring scheme. multiple alignments were performed by default value, and snp positions and the heterozygous […]

PMCID: 5686958
PMID: 29141579
DOI: 10.1186/s12711-017-0359-5

[…] pro thermocycler (eppendorf). the resulting amplicons were purified and bidirectionally sequenced by eurofins mwg (germany) using conventional sanger sequencing. variants were detected with the novosnp software []. finally, variant g.21891160g>a (krt25:p.r89h) was genotyped on an extended panel of 150 curly and 203 randomly chosen straight-haired animals from 35 different breeds using […]

PMCID: 5597596
PMID: 28904385
DOI: 10.1038/s41598-017-11523-3

[…] pro thermocycler (eppendorf). the resulting amplicons were purified and bidirectionally sequenced by eurofins mwg (germany) using conventional sanger sequencing. polymorphisms were detected with the novosnp software., for bd1, bd2 and oi, the de novo nature of the candidate mutations was confirmed using pcr and sanger sequencing in a panel of affected and unaffected animals, and dna samples […]

PMCID: 5432546
PMID: 28559908
DOI: 10.3389/fpls.2017.00791

[…] using an abi 3730 genetic analyzer according to the manufacturer’s instructions (applied biosystems, carlsbad, ca, usa) in the genomic center at purdue university. snps were identified using the novosnp program 3.0.1 microsoft windows platform version ()., the nucleotide diversity (π), nucleotide polymorphism (𝜃), and tajima’s d were analyzed with snps for each gene using tassel (). the ld […]


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novoSNP institution(s)
Department of Molecular Genetics, Flanders Interuniversity Institute for Biotechnology, University of Antwerp, Antwerpen, Belgium

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