Working with amplicon 16S Illumina and isolates strains

Question

[l.cortes.tolalpa]

Hi all!

I have sequences, 16S amplicon Illumina, from environmental samples and also I have sequences, 16S rRNA gene, from isolated strains from the same samples. I want to look for the singles isolates 16S in the amplicon sequences and know how much they match. Could you recommend me a software or tool that I can do it? Thank you for your time! Best Larisa

Answer 1

[h.mon]

Look at VSEARCH, cd-hit or USEARCH.