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Update install instructions
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Ulthran committed Jun 5, 2024
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Expand Up @@ -16,11 +16,18 @@ Primertrim requires vsearch, our recommended method of installation is through c
```bash
git clone https://github.com/PennChopMicrobiomeProgram/primertrim.git
cd primertrim
conda env create -f primertrim_env.yml -n primertrim
conda env create -f primertrim_env.yml -n primertrim
conda activate primertrim
conda install -c conda-forge -c bioconda vsearch
pip install .
```

We also have a docker image available on DockerHub:

```
docker run --rm -it ctbushman/primertrim:latest ptrim -h
```

## Algorithm

Primer detection proceeds in three stages: complete matching, partial
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