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For subsetting a sample, you can do something like this-
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Ok! I have a recommendation. I'll submit it as an answer, pending your feedback.
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OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
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Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
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[This could help][1]
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