Mapping reads to a multifasta reference

Question

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Hi all,

I would like to map reads against the card reference database (multifasta with DNA sequences for each resistance gene) but I don't seem to find the right tool to use a multifasta as a reference, could anyhone give me a hand on this one?

Thanks.

[Pierre Lindenbaum]

how do you define the "right tool" ? what did you find so far ?

[WouterDeCoster]

A multifasta file, like a eukaryotic reference genome?