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Protocols

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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Maintainer


  • person_outline Martin Corcoran

Publication for IgDiscover

IgDiscover citations

 (5)
library_books

Analyzing Immunoglobulin Repertoires

2018
Front Immunol
PMCID: 5861150
PMID: 29593723
DOI: 10.3389/fimmu.2018.00462

[…] ne 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 addi […]

library_books

Computational Strategies for Dissecting the High Dimensional Complexity of Adaptive Immune Repertoires

2018
Front Immunol
PMCID: 5826328
PMID: 29515569
DOI: 10.3389/fimmu.2018.00224

[…] of 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 germ […]

library_books

Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

2017
Front Immunol
PMCID: 5694033
PMID: 29180996
DOI: 10.3389/fimmu.2017.01433

[…] 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 (IGHV1 […]

library_books

Env Specific Antibodies in Chronic Infection versus in Vaccination

2017
Front Immunol
PMCID: 5591324
PMID: 28928737
DOI: 10.3389/fimmu.2017.01057

[…] usly 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 from […]

call_split

Data on haplotype supported immunoglobulin germline gene inference

2017
PMCID: 5502703
PMID: 28725665
DOI: 10.1016/j.dib.2017.06.031
call_split See protocol

[…] ails of sequence output and availability are outlined in . Data was pre-processed using pRESTO and Change-O as summarized in Fig. 1 in Ref. . Germline gene inference was performed using TIgGER and IgDiscover . Additional bioinformatics analysis was performed as outlined elsewhere including analysis performed using GIgGle (release 0.2) that is available under Apache License at https://github.co […]

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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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