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Align NGS result to a known sequence and quantify mismatches

Hi folks,

I'm looking for a R/python/Linux package that allow me to align NGS data in fasta to a known sequence and quanfity the mismatches.

We are testing out error prone PCR system. I plan to apply NGS to evaluate the results. Let me know if there's such packages.

Thank you. Best. Field

ngs alignment

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