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Associated diseases

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HapCompass specifications

Information


Unique identifier OMICS_00197
Name HapCompass
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.7.7
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Publication for HapCompass

HapCompass in publications

 (8)
PMCID: 5954289
PMID: 29764364
DOI: 10.1186/s12864-018-4464-9

[…] \begin{document}$o\left (2^{(k-1)n}\right)$\end{document}o2(k−1)n. therefore it is very challenging to find the optimal haplotypes., various polyploid haplotype phasing methods have been developed. hapcompass [] relied on a graphical approach to develop a scheme which resolves conflicts arising from incorrect haplotype phasing. haptree [] investigated the polyploid setup using a branch-and-bound […]

PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] using overlapping sequence reads (figure )., a number of different polyploid haplotyping tools (for sequence reads) have been developed in recent years, including polyhap (), satlotyper (), hapcompass (), haptree (), sdhap (), shesisplus (), and tripoly (motazedi et al., unpublished). three of these tools (hapcompass, haptree, and sdhap) were recently compared and evaluated over a range […]

PMCID: 5543553
PMID: 28778145
DOI: 10.1186/s12862-017-1019-7

[…] and hence are haplotype-specific by nature []. extending beyond similar approaches for diploids [, ], recent methods allow for haplotype assembly from ngs reads in polyploids [–]. for example, hapcompass, the tool we use in this study, phases haplotypes during assembly by using co-occurrence within ngs reads of alleles at different sites along a chromosome. to generate haplotypic data […]

PMCID: 4896942
PMID: 27375658
DOI: 10.3389/fpls.2016.00804

[…] genotypes were called by unified genotyper. the heterozygosity rate for each accession was estimated based on the heterozygous loci by dividing number of heterozygous sites/length of aligned region. hapcompass v0.7.7 was used for haplotype assembly with ploidy level assigned by -p (). the custom scripts were deposited in github., the snps identified above were selected for validation by sanger […]

PMCID: 4822172
PMID: 27048905
DOI: 10.1038/srep24095

[…] using the shared haplotype information within the sample, given the genotypes of individuals from a population. recently, two algorithms have been proposed for haplotype assembly: haptree and hapcompass. however, not much progress has been made recently in developing the haplotype phasing algorithms for polyploids. most of these algorithms are proposed several years ago. for example, […]


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HapCompass institution(s)
Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Inova Translational Medicine Institute, Inova Health Systems, Falls Church, VA, USA

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