MAGERI statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MAGERI
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Tool usage distribution map

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Associated diseases

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Popular tool citations

chevron_left Error correction Genome assembly Read alignment SNP detection SNV detection Demultiplexing Adapter trimming UMI processing Indel detection Variant detection Barcode removal chevron_right
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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 citations

 (3)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] et al.  clusters a UMI to its “parent” UMI that is within one edit distance and has more than six times more reads. Kou et al.  merge two UMIs within 2-base difference based on binomial probability. MAGERI clusters two UMIs that differ by one or two substitutions and whose read counts differ by 20- or 400-fold. Smith et al.  developed UMI-tools that implemented network-based UMI clustering method […]

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A high throughput assay for quantitative measurement of PCR errors

2017
Sci Rep
PMCID: 5457411
PMID: 28578414
DOI: 10.1038/s41598-017-02727-8

[…] endent 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 c […]

library_books

Exploring local knowledge and perceptions on zoonoses among pastoralists in northern and eastern Tanzania

2017
PLoS Negl Trop Dis
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. Fear […]


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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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