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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 6 |
1 files changed, 4 insertions, 2 deletions
@@ -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. |