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update README
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annacprice authored Dec 14, 2022
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# TB Pipeline #
![Build Status](https://github.com/Pathogen-Genomics-Cymru/tb-pipeline/workflows/build-push-quay/badge.svg)
![Build Status](https://github.com/Pathogen-Genomics-Cymru/tb-pipeline/workflows/pytest/badge.svg)
![Build Status](https://github.com/Pathogen-Genomics-Cymru/tb-pipeline/workflows/stub-run/badge.svg)
# Lodestone #
![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/build-push-quay/badge.svg)
![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/pytest/badge.svg)
![Build Status](https://github.com/Pathogen-Genomics-Cymru/lodestone/workflows/stub-run/badge.svg)

This pipeline takes as input reads presumed to be from one of 10 mycobacterial genomes: abscessus, africanum, avium, bovis, chelonae, chimaera, fortuitum, intracellulare, kansasii, tuberculosis. Input should be in the form of one directory containing pairs of fastq(.gz) or bam files.

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