Extract all reads from multi fasta that have a certain sequence

Hello, can anyone tell me how to extract all the reads which have a certain sequence from a multi fasta file? ‘Fasta extract sequence’ seems to only be able to extract using the Name of the sequence, not the sequence itself. All reads have the same name/ID so that isn’t usable for extracting a subset.

My situation is that I have amplicon-seq files each containing reads from 2 different PCR products, and just want to split them into 2 files using a sequence which is unique to either.


Sounds like the Filter FASTA tool is what you are looking for?

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Wonderful! Thank you so much!
That worked a treat.

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