MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences

Frontiers in Microbiology
Yue XingQunfeng Dong

Abstract

With the continued spread of SARS-CoV-2 virus around the world, researchers often need to quickly identify novel mutations in newly sequenced SARS-CoV-2 genomes for studying the molecular evolution and epidemiology of the virus. We have developed a Python package, MicroGMT, which takes either raw sequence reads or assembled genome sequences as input and compares against database sequences to identify and characterize indels and point mutations. Although our default setting is optimized for SARS-CoV-2 virus, the package can be also applied to any other microbial genomes. The software is freely available at Github URL https://github.com/qunfengdong/MicroGMT.

References

Jan 1, 1994·The Journal of General Virology·R S LanciottiD W Trent
Jan 1, 1997·Annual Review of Microbiology·E Domingo, J J Holland
Jan 31, 2004·Science·UNKNOWN Chinese SARS Molecular Epidemiology Consortium
Mar 6, 2008·Nature Reviews. Genetics·Siobain DuffyEdward C Holmes
Sep 9, 2008·Expert Opinion on Biological Therapy·Esteban DomingoVerónica Martín
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 27, 2011·Bioinformatics·Weichun HuangGabor T Marth
Jan 15, 2014·PLoS Neglected Tropical Diseases·Oumar FayeAmadou Alpha Sall
Apr 7, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Yuelong Shu, John McCauley
May 12, 2018·Bioinformatics·Heng Li
May 23, 2019·Bioinformatics·Jia-Xing Yue, Gianni Liti
Jan 10, 2017·Global Challenges·Stefan Elbe, Gemma Buckland-Merrett
Apr 2, 2020·ELife·Yinon M Bar-OnRon Milo
Apr 24, 2020·Journal of Translational Medicine·Maria PachettiRudy Ippodrino

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Methods Mentioned

BETA
GISAID

Software Mentioned

Python
Glue
bcftools
illumina
Mac
Microbial Genomics Mutant Tracker ( MicroGMT )
MicroGMT
CoV
Picard
ART

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