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SNiPloid specifications

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Unique identifier OMICS_07405
Name SNiPloid
Interface Web user interface
Restrictions to use None
License CeCILL version 2.1
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SNiPloid

SNiPloid citations

 (3)
library_books

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

2016
Genome Biol Evol
PMCID: 5633685
PMID: 27614235
DOI: 10.1093/gbe/evw209

[…] the recovery of paralogous and homoeologous copies. the constructed contigs are then compared with the diploid parental genomes using specific polymorphic sites (; ; ). pipelines such as polycat (), sniploid (), hylite () and sweep () were designed to detect homeologs in allotetraploids, using their diploid parents as reference. these tools align diploid species reads (or sequenced ests) […]

library_books

Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site‐associated markers

2016
Mol Ecol
PMCID: 4999052
PMID: 27065091
DOI: 10.1111/mec.13644

[…] arnold et al. () used ‘gatk’ (mckenna et al. ) to genotype biallelic snps in autotetraploid arabidopis arenosa. other recent methods such as ‘hands’ (mithani et al. ), ‘polycat’ (page et al. ) and ‘sniploid’ (peralta et al. ) assign snp alleles to specific subgenomes of allopolyploids, relying on data from known diploid progenitors. we decided to construct our own pipeline for the current paper […]

library_books

Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms

2015
BMC Genet
PMCID: 4423573
PMID: 25951770
DOI: 10.1186/1471-2156-16-S2-S4

[…] multiple snps overlapped by a single read are evaluated for consistency of the genome assignment. other tools have been developed using similar approaches to this problem, including hands and sniploid [,]., along with read categorization, a researcher should consider a few issues when analyzing sequence data from an allopolyploid. first, if diploid a is used as the reference sequence, […]


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SNiPloid institution(s)
UMR RPB, IRD (Institut de Recherche pour le Développement), Montpellier, France

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