POLYBAYES protocols

View POLYBAYES computational protocol

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POLYBAYES specifications

Information


Unique identifier OMICS_14876
Name POLYBAYES
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gabor Marth <>

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Publication for POLYBAYES

POLYBAYES in pipelines

 (5)
2013
PMCID: 3816612
PMID: 24144082
DOI: 10.1186/1471-2164-14-721

[…] using the primer3 program []., snps in the est sequences among the different radish cultivars were identified as described in clepet et al. []. briefly, polymorphisms were first identified with polybayes [] and only those with at least 2× coverage for each accession and no same bases at the potential snp site between the two compared accessions were considered. detailed information related […]

2011
PMCID: 3118787
PMID: 21599934
DOI: 10.1186/1471-2164-12-252

[…] tetra-, penta- and hexa-nucleotide. primer pairs flanking each ssr loci were designed using the primer3 program []., snps in the cdna sequences between different melon cultivars were identified with polybayes [], which takes into account both the depth of the coverage and quality of the bases. to further eliminate errors introduced by pcr amplification during the cdna synthesis step […]

2011
PMCID: 3150297
PMID: 21756356
DOI: 10.1186/1471-2105-12-287

[…] a variety of approaches exist for calling snps from non-overlapping pooled samples, e.g. varscan [], crisp [], snpseeker [], the maq alignment tool [], and others; and non-pooled samples, e.g. polybayes [], polyscan [], the method by stephens et al. [], and others. our approach, camba, is specifically geared to working on pooled experiments with overlap between the dna pools, i.e. dna […]

2010
PMCID: 2897810
PMID: 20565788
DOI: 10.1186/1471-2164-11-384

[…] in a compound microsatellite was 100 bp. primer pairs flanking each ssr loci were designed using the primer3 program []. snps in the cdna sequences between wi1983g and wi1983h were identified with polybayes []. to eliminate errors introduced by pcr amplification during the cdna synthesis step and homopolymer errors introduced by the 454 pyrosequencing technology, and to distinguish true snps […]

2005
PMCID: 1239908
PMID: 16146575
DOI: 10.1186/1471-2105-6-220

[…] base quality score in the perfect block; 90%, minimum percent identity for query-anchor alignments; 97%, minimum percent identity for the highly similar regions of query-anchor alignments., although polybayes was not designed to deal with data sets of deep coverage, we tested polybayes on the eighteen data sets of deep coverage to see how polybayes would behave on the data sets. […]


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POLYBAYES in publications

 (34)
PMCID: 4369683
PMID: 25848168
DOI: 10.6026/97320630011085

[…] and/or output formats, computational algorithms, filtration and evaluation strategies for getting quality snps. there are many programs and pipelines for detection of snps viz; sean [] polyphred [] polybayes [] trace_diff [], harvest [], autosnp [], qualitysnp [] qualitysnpng []. qualitysnp has three filtering system to eliminate unreliable variations and to handle typical sequencing errors […]

PMCID: 3817360
PMID: 24204379
DOI: 10.3389/fgene.2013.00226

[…] non-rjf reads that we set for snp detection including the total number of reads from both lines (i.e., ~24× depth coverage) to increase the sensitivity. the gigabayes software, a newer version of polybayes (), was used for snp calling., we applied the flanking-snp-value (fsv) method () to the resequencing data from the hws and lws lines across the selected qtl regions. the fsv method computes […]

PMCID: 3827885
PMID: 24175923
DOI: 10.1186/1471-2164-14-746

[…] (pipelines) have been developed for automatic snp mining, using different input data, computational algorithms, quality evaluation strategies, and/or output formats. for example, the polyphred and polybayes pipeline typically requires sequence trace files or extracted sequences with base calling quality values to minimize false snps resulting from sequencing errors [-]. polybayes also includes […]

PMCID: 3816612
PMID: 24144082
DOI: 10.1186/1471-2164-14-721

[…] using the primer3 program []., snps in the est sequences among the different radish cultivars were identified as described in clepet et al. []. briefly, polymorphisms were first identified with polybayes [] and only those with at least 2× coverage for each accession and no same bases at the potential snp site between the two compared accessions were considered. detailed information related […]

PMCID: 3557274
PMID: 23382983
DOI: 10.1371/journal.pone.0054835

[…] base-recalling) after the primary sequence has been defined. to avoid misinterpreting sequencing artifacts as single nucleotide polymorphisms (snps), a number of algorithms, like polyphred , , polybayes , and autoeditor , require pre-assembled dna sequences of various individual genomes. these algorithms are designed for resequencing eukaryotic genomes with a low degree of variability, […]


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POLYBAYES institution(s)
Department of Genetics and Genome Sequencing Center, Washington University, St Louis, MO, USA; Division of Dermatology, St Louis, MO, USA
POLYBAYES funding source(s)
This work was supported by NIH grants P50HG01458, R01HG1720 and T32AR07284, and Compaq Computer Corporation.

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