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Update README.md
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marcelauliano authored Apr 12, 2022
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Expand Up @@ -156,7 +156,7 @@ Using the species in our test data as an example, you would do:
```
findMitoReference.py --species "Phalera bucephala" --email [email protected] --outfolder /data/ --min_length 16000
```
This command will give you NC_016067.1.fasta and NC_016067.1.gb that you can be used for flags **-f** and **-g** in the main pipeline.
This command will give you NC_016067.1.fasta and NC_016067.1.gb that you can uese for flags **-f** and **-g** in the main pipeline.

2-) Now, you need to decide if you want to run MitoHiFi v2.2 from:
(i) raw reads, in which case the pipeline will map the reads (flag **-r**) to the reference genome of the closely-related species to pull out mito-reads and exclude possible NUMTS and then assemble them using Hifiasm, or
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