MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences
Yue Xing, Xiao Li, Xiang Gao, Qunfeng 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.
Topics & Concepts
GenomeIndelPython (programming language)BiologyComputational biologyGeneticsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Whole genome sequencingGenomicsMutationBacterial genome sizePoint mutationCoronavirus disease 2019 (COVID-19)GeneComputer scienceInfectious disease (medical specialty)Single-nucleotide polymorphismMedicineDiseasePathologyGenotypeOperating systemSARS-CoV-2 and COVID-19 ResearchBacteriophages and microbial interactionsGenomics and Phylogenetic Studies