discoSnp++ protocols

discoSnp++ specifications

Information


Unique identifier OMICS_00267
Name discoSnp++
Alternative names Discovering Single Nucleotide Polymorphism, DiscoSnp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License CeCILL version 2.1, GNU Affero General Public License version 3
Computer skills Advanced
Version 2.3.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Pierre Peterlongo <>
  • person_outline Jeremy Gauthier <>

Publication for Discovering Single Nucleotide Polymorphism

discoSnp++ IN pipelines

 (5)
2016
PMCID: 4758021
PMID: 26892170
DOI: 10.1186/s12864-016-2447-2

[…] m.truncatula, a.thaliana and glycine max ncbi) and chloroplastic (from pea ncbi refseq nc_014057.1) contamination. low complexity sequences were finally removed using a custom perl script., the discosnp tool [24] calls snps from one or several read sets without using a reference genome or any other source of information. discosnp aims to predict isolated snps (well suited for being easily […]

2016
PMCID: 4758021
PMID: 26892170
DOI: 10.1186/s12864-016-2447-2

[…] sequences were finally removed using a custom perl script., the discosnp tool [24] calls snps from one or several read sets without using a reference genome or any other source of information. discosnp aims to predict isolated snps (well suited for being easily amplified by pcr), k nucleotides apart from any other polymorphism source, with k being the main parameter. a micro assembly […]

2016
PMCID: 4758021
PMID: 26892170
DOI: 10.1186/s12864-016-2447-2

[…] by a pair of sequences which differ only at the polymorphic site. each sequence comment provides information on average read coverage and average read quality per input read set. we applied the discosnp tool to cleaned reads from four pea lines (‘baccara’ , ‘pi180693’ , ‘champagne’ and ‘terese’), with “k-mer = 27” as the input parameter, which was empirically shown to maximize the number […]

2016
PMCID: 4758021
PMID: 26892170
DOI: 10.1186/s12864-016-2447-2

[…] ‘pi180693’ , ‘champagne’ and ‘terese’), with “k-mer = 27” as the input parameter, which was empirically shown to maximize the number of predictions in our conditions [24]. the kissreads module of the discosnp tool provides the coverage for each snp on the reads for each ril. a dedicated perl script then enchained several filters to retain only the most reliable snps based on available sequence dat […]

2016
PMCID: 4758021
PMID: 26892170
DOI: 10.1186/s12864-016-2447-2

[…] allele., robust snps (highly or very highly designable for genotyping assay designs) polymorphic between the ‘baccara’ and ‘pi180693’ parental lines were inferred using the kissreads module of the discosnp tool [24] on cleaned reads generated by sequencing the 48 ‘baccara’ x ‘pi180693’ rils. kissreads provides the coverage for each snp on reads for each ril. considering that less sequence data […]

discoSnp++ institution(s)
IRISA Inria Rennes Bretagne Atlantique, GenScale team, Rennes, France; CHU Pontchaillou, Rennes, France
discoSnp++ funding source(s)
Supported by the French ANR-12-BS02-0008 Colib’read project and by the ANR-12-EMMA-0019-01 GATB project.

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