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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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Publication for Discovering Single Nucleotide Polymorphism

discoSnp++ citations

 (4)
call_split

Beaver Fever: Whole Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

2018
PMCID: 5917422
PMID: 29695621
DOI: 10.1128/mSphere.00090-18
call_split See protocol

[…] WB, DH_A, and GS_B, using BLASTn megablast, with the same parameters as described above, and reads which hit only the majority assemblages were removed. The remaining reads were then included in the discoSNP analysis as below.Single nucleotide variant (SNV) calling was performed by entering trimmed reads into discoSNP v2.1.2 () with parameters -c 4 –b 1 –k 31 –P 3, and a separate run for each ass […]

library_books

SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

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

[…] 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 [] 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 wa […]

library_books

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

2016
GigaScience
PMCID: 4750246
PMID: 26870323
DOI: 10.1186/s13742-015-0105-2

[…] may be wrong (with a controlled percentage).Thus, the bloom filter representation has the main advantage of a very low memory footprint. For instance, nearly 3 billion reads (100 bp) were analyzed by DISCOSNP, using at most 5.7 GB of memory. Moreover, the low memory footprint does not imply a degradation in the running time. The COMMET tool, being a heuristic based only on a bloom filter, is also […]

library_books

Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS based mapping and positional cloning approaches

2015
Front Plant Sci
PMCID: 4333798
PMID: 25745426
DOI: 10.3389/fpls.2015.00068

[…] d to be 3.7 × sd and 5.9 × sd lower than the average, respectively. This shows that less (if any) SNPs are detected in these regions because their high variability prevents the identification of what discoSNP names a SNP: a region of 61 consecutive residues among which only the central base differs between the two strains. What lacks in these highly variable regions is not the differing base, but […]

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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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