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MiGEC specifications

Information


Unique identifier OMICS_04055
Name MiGEC
Alternative name Molecular Identifier Groups-based Error Correction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Molecular Identifier Groups-based Error Correction

MiGEC citations

 (14)
library_books

Analyzing Immunoglobulin Repertoires

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

[…] ure A). A number of UMI-based methods have been devised to improve sequence quality (Figures B–D) or identify PCR bias (Figure E)—discussed here.The Molecular Identifier Group based Error Correction (MIGEC) groups similar sequences with same UMI and uses a set of rules to predict errors (). One rule is to identify a consensus sequence based on the most common variant within a UMI group. However, i […]

library_books

Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification

2018
Front Immunol
PMCID: 5808239
PMID: 29467754
DOI: 10.3389/fimmu.2018.00033

[…] a single cell in as many as one million naïve T cells; and (4) the ability to quantify T cell clonal expansion due to infection in CMV-seropositive patients.Previous MID-based IR-seq methods, such as MIGEC, build TCR consensus sequences by grouping MIDs (, ). However, the number of target molecules could vary significantly with different sample inputs, which could be challenging for choosing the a […]

library_books

Immune Repertoire after Immunization As Seen by Next Generation Sequencing and Proteomics

2017
Front Immunol
PMCID: 5650670
PMID: 29085363
DOI: 10.3389/fimmu.2017.01286

[…] ll 10 samples was multiplexed in a single MiSeq run. Sequencing data were demultiplexed on index as well as PCR primer. Paired end reads were combined with PEAR and, subsequently, assembled using the MIGEC () pipeline, which processes the molecular barcode information for sequence error correction and to report expression levels without PCR bias. Default parameters were used except a minimum UMI c […]

library_books

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

2017
Front Immunol
PMCID: 5643411
PMID: 29075258
DOI: 10.3389/fimmu.2017.01267

[…] ge abundances (>100) was decreased following error correction. We compared the results of our analysis pipeline on this sample to an analysis of the same sample using another UMI-based analysis tool, MIGEC (). Both the total number of UMIs detected, the number of unique TCRs and the clonal distribution of the corrected data, were similar for the two methods (see Table S4 and Figure S7 in Supplemen […]

library_books

Heterogeneity of tumor infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi omics analysis of glioblastoma multiforme

2017
Sci Rep
PMCID: 5537248
PMID: 28761058
DOI: 10.1038/s41598-017-05538-z

[…] momatic. Then, we used FLASH to merge the paired reads to obtain the complete sequence of the CDR3 regions. To assign the rearranged mRNA sequences to their germline V, D, and J counterparts, we used MiGEC. We used VDJtools to accomplish the basic statistics and diversity analysis (calculation of the Shannon-Wiener diversity index (hereafter, ShannonDI)) of the TCR clones. […]

library_books

Overview of methodologies for T cell receptor repertoire analysis

2017
BMC Biotechnol
PMCID: 5504616
PMID: 28693542
DOI: 10.1186/s12896-017-0379-9

[…] provides TCR diversity measures and gene usage statistics computations is the R package “tcR”, which can be used to process the output files format of software as ImmunoSEQ [, ], IMSEQ, MiTCR, MiXCR, MIGEC and VDJtools []. Other approaches recently developed for estimation of TCR diversity are from Greiff et al., which creates a diversity profile using many diversity coefficients simultaneously [] […]


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MiGEC institution(s)
Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic

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