Commit a3441a05 authored by peguerin's avatar peguerin
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readme update

parent 805ad789
......@@ -78,6 +78,7 @@ You can use the absolute path of the folder of your reference database as the `/
* [nextflow_obitools](https://gitlab.mbb.univ-montp2.fr/edna/nextflow_obitools)
* [snakemake_only_obitools](http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools)
## Reference database in STAMPA format
Once you generated your reference database, you need the `db_{prefix}.fasta` file (see Results section above).
......@@ -89,6 +90,19 @@ This command generates a file `/path/to/reference_database_stampa.fasta` which y
* [bash_swarm](https://gitlab.mbb.univ-montp2.fr/edna/bash_swarm)
# Build a reference database (RAPIDRUN)
1. Write a table [infos/markers.csv](infos/markers.csv) with name of marker, primer 5' and primer 3'
2. Fill configuration field into [config.sh](config.sh)
3. Execute main script
```
bash build_bdr_rapidrun.sh
```
This will generate a folder for each marker with a database of reference sequences belonging to the marker sequences.
# Authors
* Pierre-Edouard GUERIN, CNRS, CEFE
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