Bact-Builder: a new streamlined tool for generating high quality consensus based, complete Mycobacterium tuberculosis genomes

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB). Mtb was responsible for over 1 million deaths in 2020 (WHO, 2020). Whole Genome Sequencing (WGS) for Mtb is increasingly being used to track and treat Mtb infections. These efforts rely on complete and accurate genomes. There is no gold-standard approach for assembling Mtb genomes. Current tools are not consistent, reliable or robust and typically use a single assembler approach. Here we present Bact-Builder – a new streamlined tool that enables end to end de novo assembly of bacterial genomes. Using Bact-Builder we have identified 10 key regions of difference between the published H37Rv reference strain and laboratory strains and now propose an updated reference sequence for H37Rv

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