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Update docs/usage.md
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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danilodileo and jfy133 authored Sep 27, 2024
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Expand Up @@ -131,7 +131,7 @@ nextflow run nf-core/magmap -profile docker --outdir results/ --input samples.cs

### Sourmash (optional)

with [Sourmash](https://sourmash.readthedocs.io/en/latest/index.html) you can filter the genomes to be used by magmap in the mapping step. This function is optional but can speed up the process and let you get a better genomes /reads mapping ratio since you are removing all the genomes that are not passing the threshold (that you can select).
With [Sourmash](https://sourmash.readthedocs.io/en/latest/index.html) you can filter the genomes to be used by magmap in the mapping step. This function is optional but can speed up the process and let you get a better genomes /reads mapping ratio since you are removing all the genomes that are not passing the threshold (that you can select).

```bash
nextflow run nf-core/magmap -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv --sourmash true
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