Subsample fasta per taxon
Hello, I have some fasta files downloaded from NCBI, containing sequences of numerous taxa each, and I would like to reduce the amount of sequences per file, i.e. pull out a fixed number of sequences per genus (or per family). I suppose its a standard operation, but I failed to find the correct approach. I have tried the obitools options obisample and obiselect, but I don't see how to specify the 'per genus' option from the taxonomy (if there is one). Perhaps someone can give me a hint what other tool (or syntax) to use for this. Any help greatly appreciated!
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Does your fasta file have a species identified in the header? Can you post a few lines from the file here?
it looks like this -