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Protocols

Exome-assistant specifications

Information


Unique identifier OMICS_29983
Name Exome-assistant
Interface Web user interface
Restrictions to use None
Input data The SNPs/InDels calling results, which are generated by SNPs/InDels calling tools.
Input format VCF,PILEUP
Programming languages Perl, PHP
Computer skills Basic
Maintained No

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Publication for Exome-assistant

Exome-assistant citations

 (3)
library_books

A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia

2016
Hum Genome Var
PMCID: 4899602
PMID: 27330822
DOI: 10.1038/hgv.2016.9

[…] the Burrows–Wheeler Aligner to identify insertions and deletions (InDels) using the genome analysis toolkit program. The identified single-nucleotide polymorphisms and InDels were annotated using the Exome-assistant program (http://122.228.158.106/exomeassistant). The MagicViewer software was used to view the short-read alignments and validate the candidate single-nucleotide polymorphisms and InDe […]

call_split

Whole exome sequencing identifies USH2A mutations in a pseudo dominant Usher syndrome family

2015
PMCID: 4564089
PMID: 26310143
DOI: 10.3892/ijmm.2015.2322
call_split See protocol

[…] ified SNPs, were analyzed using the Picard software and SOAPsnp program, respectively. Variants of the Indels were identified using the GATK program. All the identified variants were annotated by the exome-assistant program (). In addition, the variants with a frequency >1% were removed and the SIFT (http://sift.jcvi.org/www/SIFT_enst_submit.html), PolyPhen (http://genetics.bwh.harvard.edu/pph2/) […]

library_books

Identification of Three Novel Mutations in the FRMD7 Gene for X linked Idiopathic Congenital Nystagmus

2014
Sci Rep
PMCID: 3894538
PMID: 24434814
DOI: 10.1038/srep03745

[…] utadapt (http://code.google.com/p/cutadapt/), SOAP aligner, BWA and GATK programs to retrieve and align to identify SNPs and insertions or deletions (InDels). SNPs and InDels were annotated using the exome-assistant program (http://122.228.158.106/exomeassistant). We selected the CASK gene (NM_001126054) for the mutation survey. […]

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Exome-assistant institution(s)
Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China; Beijing Institutes for Biological Sciences, Chinese Academy of Science, Beijing, China
Exome-assistant funding source(s)
Supported by the National Natural Science Foundation of China (Grant No. 31100917; Grant No. 31171236) and International S&T Cooperation Program of China (2011DFA30670,).

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