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MAGERI specifications

Information


Unique identifier OMICS_18136
Name MAGERI
Alternative name Molecular tAgged GEnome Re-sequencing pIpeline
Software type Package/Module
Interface Command line interface
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Dmitriy Chudakov <>

Publication for Molecular tAgged GEnome Re-sequencing pIpeline

MAGERI in publications

 (4)
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] consensus), resulting in remarkably higher specificity compared to raw-reads-based variant calling.fig. 1, currently, three umi-based variant callers are available in public domain: deepsnvminer, mageri, and smcounter , , . deepsnvminer first generates an initial list of variants using samtools calmd and then selects the high-confidence variants with strong umi support. mageri builds […]

PMCID: 5460480
PMID: 28583065
DOI: 10.1186/s12864-017-3815-2

[…] pcr product was used in case of exoi treatment. the resulting libraries of egfr gene fragment were analyzed using paired-end hiseq2500 illumina sequencing., data analysis was performed using our mageri software designed to analyze umi-tagged targeted genome re-sequencing data []. in this back-to-back comparison starting with identical amounts of dna, nope method outperformed exoi method […]

PMCID: 5457411
PMID: 28578414
DOI: 10.1038/s41598-017-02727-8

[…] experiments measuring both the linear amplification and pcr error rates from 20 cycles. additionally, sequencing data were obtained for an unamplified library. datasets were analyzed using the mageri (https://github.com/mikessh/mageri) pipeline. briefly, umi tags were extracted and tags that were read less than five times were filtered, as these would not provide enough consensus sequence […]

PMCID: 5325590
PMID: 28146556
DOI: 10.1371/journal.pntd.0005345

[…] the meat is good to eat or not but we cannot just eat a meat of animal we find dead. we ask the boy who was herding what happened to it. but it is still difficult to know sometimes.” (fgd-01-male-03-mageri village, ngorongoro), while most of the discussions and interviews suggested fearlessness in the consumption of meat from known sick animals, it seems there was a limit to that fearlessness. […]


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MAGERI institution(s)
Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Evrogen JSC, Moscow, Russia; Skolkovo Institute of Science and Technology, Moscow, Russia
MAGERI funding source(s)
Supported by Russian Science Foundation grant №14-35-00105, by RFBR grant 15- 34-21052, by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601), by European Union’s Horizon 2020 research and innovation programme under grant agreement No 633592 (APERIM).

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