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@@ -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. | ||
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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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