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IgDiscover specifications

Information


Unique identifier OMICS_16456
Name IgDiscover
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An RNA sequence (raw).
Input format FASTQ, FASTA
Output data A gene expression profile.
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.6.0
Stability Stable
Maintained Yes

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  • person_outline Martin Corcoran <>

Publication for IgDiscover

IgDiscover in publications

 (6)
PMCID: 5861150
PMID: 29593723
DOI: 10.3389/fimmu.2018.00462

[…] databases. humans and mice have the most well defined ig gene loci, but a map of all allelic variants is not complete (). there have been efforts to address this with algorithms—such as tigger (), igdiscover (), impre (), and a more recent allele prediction and validation tool ()—that can be used to identify germline alleles for individual repertoires. proper identification of non-template […]

PMCID: 5826328
PMID: 29515569
DOI: 10.3389/fimmu.2018.00224

[…] using one central germline reference database containing a more or less static set of non-personalized germline gene alleles. to address this problem, corcoran et al. developed a software package (igdiscover), which employs a cluster identification approach to reconstruct de novo from an airr-seq data set the corresponding v-gene germline database—all without a priori knowledge of existing […]

PMCID: 5694033
PMID: 29180996
DOI: 10.3389/fimmu.2017.01433

[…] the number of sequences at different stages of the analysis pipeline is provided in supplementary table eiv in levin et al. ()., the germline gene repertoire of the donors have been inferred using igdiscover () using the igm-encoding transcriptomes of the donors’ bm, and has, when possible, been quality controlled by haplotype-based analysis (, ). eleven commonly expressed germline genes […]

PMCID: 5591324
PMID: 28928737
DOI: 10.3389/fimmu.2017.01057

[…] appreciated (–). an improved understanding of human antibody germline genes is therefore needed. we recently reported that next-generation sequencing (ngs) coupled with a new computational tool, igdiscover, can accelerate the definition of germline-encoded ig gene segments and allow higher-throughput studies ()., hiv-1 bnab sequences stand out not only because of high levels of divergence […]

PMCID: 5647986
PMID: 28786733
DOI: 10.1080/21645515.2017.1353852

[…] protein based immunizations. gunilla karlsson hedestam (karolinska institutet) presented a method of determining individual vh germline repertoires using next generation sequencing. this method (igdiscover) was used to elucidate the germline b-cell repertoires of rhesus macaques and healthy human volunteers demonstrating a higher level of variation among individuals and identifying multiple […]


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IgDiscover funding source(s)
This work was funded by an NIH P01 grant AI104722 (HIVRAD) and a grant from the International AIDS Vaccine Initiative (IAVI), a Karolinska Institutet KID grant, Knut and Alice Wallenberg Foundation to the Wallenberg Advanced Bioinformatics Infrastructure.

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