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perEditor specifications

Information


Unique identifier OMICS_16538
Name perEditor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference DNA sequence, a file containing SNPs and indels information in VCF, the maternal or paternal allele used to build the new reference sequence, the particular individual among all the samples presented in the VCF file.
Input format FASTA, VCF
Output data The maternal and paternal alleles of the individual genome.
Output format FASTA
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Sheng Zhong

Publication for perEditor

perEditor citation

library_books

One Size Doesn't Fit All RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

2015
PLoS Comput Biol
PMCID: 4534450
PMID: 26267278
DOI: 10.1371/journal.pcbi.1004448

[…] d reference genome strategy very attractive.There are tools available for constructing personal genomes that integrate known variants into the reference genome such as vcf2diploid in AlleleSeq [] and perEditor []. Compared to these existing tools, there are several unique characteristics and contributions of RefEditor. First the purpose of RefEditor is to enable precision variant calling and disco […]


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perEditor institution(s)
Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
perEditor funding source(s)
This work was supported by NIH DP2-OD007417, NSF DBI 08-45823, NSF DBI 09-60583.

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