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mtisza1 committed May 30, 2023
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Read mapping pipeline for detection and measurement of human and animal virus pathogens from short read metagenomic environmental or clinical samples.

This approach is sensitive, specific, and ideal for exploring virus presence/absence/diversity within and between metagenomic or clinical samples. Interactive reports make it easy to see the breadth of read coverage for each detected virus. This tool should reliably detect virus genomes with 90% ANI or greater to reference genomes.


NOTE: The database used by `Esviritu` should cover all human and animal viruses in GenBank as of November 16th, 2022 (EsViritu DB v2.0.2). However, the genomes are dereplicated at 95% ANI so that only one genome from a nearly identical group is used. Please open an issue to report any omissions.

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Remember to set `-f True` to run the filtering step.


### Step-by-step Description of Pipeline
## Step-by-step Description of Pipeline

- inputs are .fastq files

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