https://github.com/mikessh/mageri

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
https://github.com/mikessh/mageri

amplicon bioinformatics cancer ctdna exon mapping mutation umi variant

Last synced: about 1 month ago
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MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

• Host: GitHub
• URL: https://github.com/mikessh/mageri
• Owner: mikessh
• License: other
• Created: 2014-11-19T11:40:59.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2017-05-08T22:17:54.000Z (about 9 years ago)
• Last Synced: 2026-01-15T08:17:35.602Z (5 months ago)
• Topics: amplicon, bioinformatics, cancer, ctdna, exon, mapping, mutation, umi, variant
• Language: Java
• Homepage: http://mageri.readthedocs.org/en/latest/
• Size: 99.7 MB
• Stars: 21
• Watchers: 5
• Forks: 6
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
MAGERI

======

[![Build Status](https://travis-ci.org/mikessh/mageri.svg?branch=master)](https://travis-ci.org/mikessh/mageri)

[Molecular tagging approach](http://www.pnas.org/content/108/23/9530) has revolutionized the field of high depth genome re-sequencing 

by allowing detection of ultra-rare mutations. This pipeline aims at filling the gap in software for analysis of UMI-tagged data. 

MAGERI implements consensus assembly, alignment and variant calling and allows to process 

datasets into ready SAM and VCF files in a single command. Its main purpose is to analyze targeted region genome re-sequencing data for tumor heterogeneity and circulating tumor DNA studies, however it can be also applied to other tasks that require accurate rare variant detection.

See [mageri-paper repository](https://github.com/mikessh/mageri-paper) for examples and supplementary data.

Software binaries can be found in the [releases section](https://github.com/mikessh/mageri/releases/latest), the documentation is available [here](http://mageri.readthedocs.io/en/latest/).

Please cite the software as [Shugay et al. Plos Comp Biol 2017](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005480).