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ASEQ specifications

Information


Unique identifier OMICS_10010
Name ASEQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License MIT License
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Francesca Demichelis

Publication for ASEQ

ASEQ citations

 (6)
library_books

EthSEQ: ethnicity annotation from whole exome sequencing data

2017
PMCID: 5818140
PMID: 28369222
DOI: 10.1093/bioinformatics/btx165

[…] also provided by EthSEQ. The target model is created either from the input list of individual’s germline BAM files that are genotyped at all reference model’s positions using the genotyping module of ASEQ () (depth of coverage ≥ 10X and read/base mapping qualities ≥ 20 here required by default to guarantee confident genotype calls) or from genotypes provided as input to EthSEQ in VCF format.Princi […]

library_books

No Excess of Cis Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus)

2017
Genome Biol Evol
PMCID: 5381623
PMID: 28137746
DOI: 10.1093/gbe/evx004

[…] Following the method implemented in the ASEQ tool (), we first performed a binomial test to identify the positions at which the ratio of the two alleles in the transcriptomic data is significantly different from 0.5. Then we assessed the re […]

library_books

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

2016
Nucleic Acids Res
PMCID: 5952581
PMID: 27899656
DOI: 10.1093/nar/gkw1076

[…] oinformatics 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 family trio data (e.g. AlleleSeq and Allim) are required for haplotyping using most of th […]

library_books

Simul seq: combined DNA and RNA sequencing for whole genome and transcriptome profiling

2016
Nat Methods
PMCID: 5734913
PMID: 27723755
DOI: 10.1038/nmeth.4028

[…] To examine LOH at the level of gene expression, allele-specific expression (ASE) in the tumor RNA was calculated for heterozygous positions called in the normal using ASEQ. Briefly, GENOTYPE mode was run on a bam file derived from the paired normal genome with the following options: mbq = 20 mrq = 1 mdc = 5 htperc = 0.2. Next, ASE mode was run using a bam file from […]

library_books

Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

2016
Nat Med
PMCID: 4777652
PMID: 26855148
DOI: 10.1038/nm.4045

[…] then estimate tumor ploidy. Next, a local optimization approach based on putative clonal mono-allelic deletions and germline heterozygous SNP loci (called informative SNPs and identified by means of ASEQ) is applied to assess the purity (1-admixture) of each sample; the difference between observed and expected allelic fraction (AF) at informative SNPs (the latter being either 0 or 1) is proportio […]

library_books

Tools and best practices for data processing in allelic expression analysis

2015
Genome Biol
PMCID: 4574606
PMID: 26381377
DOI: 10.1186/s13059-015-0762-6

[…] eads. Runtime benchmarking was performed using 100 %, 75 %, and 50 % of the reads sampled from the file, and is reported as the mean of 10 runs with the 95 % confidence interval shown. For comparison ASEQ v.1.1.8 was run in pileup mode. Benchmarking was run on CentOS 6.5 with Java version 1.6 on an Intel Xeon CPU E7- 8830 @ 2.13GHz. […]

Citations

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ASEQ institution(s)
Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
ASEQ funding source(s)
Department of Defense (PC094516 and PC101020P2); National Cancer Institute (R01CA152057); the Associazione Italiana per la Ricerca sul Cancro (AIRC, IG 13562)

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