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Using the full pipeline with Snakemake

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Andrew Zheng edited this page Mar 12, 2023 · 8 revisions

If the user only has reads and references and wants to generate a SAM file, we outline the steps to also download and use an initial aligner such as Bowtie2, Pathoscope2, or minimap2.

Installing Initial Aligners

To download the initial aligners, run the following command to download all three initial aligners.

bash install.sh

If you do not want to download some of the aligners, open and comment out the respective lines in the install.sh file.

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