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@@ -40,7 +40,7 @@ Note that you will need to repeat the `. venv/bin/activate` step from this direc
Install from PyPi:
```sh
-pip3 bh20-seq-uploader
+pip3 install bh20-seq-uploader
```
Install from git:
@@ -146,9 +146,11 @@ For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL
Run the uploader with a FASTA or FASTQ file and accompanying metadata file in JSON or YAML:
```sh
-bh20-seq-uploader example/sequence.fasta example/metadata.yaml
+bh20-seq-uploader example/metadata.yaml example/sequence.fasta
```
+If the sample_id of your upload matches a sample already in PubSeq, it will be considered a new version and supercede the existing entry.
+
## Workflow for Generating a Pangenome
All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself.