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AlleleSeq specifications


Unique identifier OMICS_05503
Name AlleleSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Joel Rozowsky

Publication for AlleleSeq

AlleleSeq citations


Liquid phase sequence capture and targeted re sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway

Sci Rep
PMCID: 5514110
PMID: 28717173
DOI: 10.1038/s41598-017-06120-3
call_split See protocol

[…] tream analysis.PredictSNP and Provean were used to predict possible impact of amino acid substitutions/deletions on the structure and function of proteins.The vcf2diploid tool, version 0.2.6a ( was used to reconstruct genotype-specific target genomic. Cis-acting regulatory DNA elements within the putative regulatory regions of the 34 candidate genes were […]


The genetic basis of parental care evolution in monogamous mice

PMCID: 5600873
PMID: 28424518
DOI: 10.1038/nature22074

[…] s Genome Project (Pman_1.0, GenBank accession: GCA_000500345.1). We created a P. polionotus genome and annotation by incorporating SNPs and indels into the P. maniculatus Pman_1.0 reference using the AlleleSeq package and the UCSC liftover tool. Briefly, P. polionotus gDNA reads (Genbank BioProject accession: PRJNA53593) were aligned to the Pman_1.0 reference using Stampy v1.0.21 with a substituti […]


Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease

Hum Mol Genet
PMCID: 5886188
PMID: 28335003
DOI: 10.1093/hmg/ddx092

[…] ch allele separately (,,) and to identify allele-specific binding events showing a significant difference in the number of mapped reads between parental alleles. We employed a modified version of the AlleleSeq pipeline () to carry out the VDR-ASB analysis. Briefly, we tested for significant allelic imbalance among all read pile-ups intersecting a variant showing heterozygous genotype, given a null […]


IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing

Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] e-wide ASE with less bias while not being limited to only known SNVs (). A number of bioinformatics tools based on high-throughput Second Generation Sequencing (SGS) data have been developed, such as AlleleSeq (), MMSEQ (), asSeq (), Allim (), MBASED (), Allele Workbench (), QuASAR (), ASEQ (), EMASE () and others (,,). However, either available phased genotypes (e.g. MMSEQ, asSeq and EMASE) or fa […]


A haplotype based normalization technique for the analysis and detection of allele specific expression

BMC Bioinformatics
PMCID: 5020486
PMID: 27618913
DOI: 10.1186/s12859-016-1238-8

[…] anel. SNVs and Indels not on the reference panel were assigned randomly to one of the two haplotypes. Parental genomes for the simulated individual were generated using the vcf2diploid program within AlleleSeq [] and parental GTF files were created using the output files and liftOver tool. We then mapped the simulated data to both parental genomes using the same mapping tools and filtering pipelin […]


A uniform survey of allele specific binding and expression over 1000 Genomes Project individuals

Nat Commun
PMCID: 4837449
PMID: 27089393
DOI: 10.1038/ncomms11101

[…] f the overlapping SNVs matches the nucleotide on the corresponding read, as they suggest sequencing errors. Apart from the AlleleDB implementation, we also introduced an alternative approach into the AlleleSeq pipeline to account for AMB, where we explicitly check for multi-mapping reads at loci with allelic imbalance (details are given in ). […]


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AlleleSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

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