Map to reference

I try to characterize strains of the endosymbiont Wolbachia using the sequences of six conserved genes as molecular markers to genotype a strain.
In my case the endosymbiont is within a flea so i extract the DNA from the fleas and each flea referee as one sample that include all the six genes of the endosmbiont,
I amplified each gene separately using PCR and mix all the six together to one sample that was sequenced using illumina paired end 2X250bp. Now I want to separate each sample by using map to reference so I will get six different file each one include one gene. Afterward I want to look for SNPs within each gene.


Hi @Ron_Flatau,
You can use exclude-seqs to align your representative sequences to a reference and thus split out by gene. This step would be done after you have dereplicated/denoised your data.

I hope that helps!

The representative sequences don’t include all the sequence that I have in my sample. There is a way to align to reference before dereplicated/denoised my data?


Not in QIIME 2. That would be an operation on the raw data, which you can perform prior to importing to QIIME 2.

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