I know that there are many software (QIIME,mothur, and others ) to analysis amplicon sequence data for microbial (SPECIALLY FOR BACTERIA). I am currently doing amplicon sequencing using 200 loci specific primers for malaria parasites (Vivax). 200 primers were designed for each locus and multiplex at least 10 primers in primary PCR. I,e a total of 20 PCR reactions. 2nd secondary PCR was done to add sample specific barcodes and Illumina index primers for library preparations and sequenced using MiSeq Illumina. So what would be the best software to analyze this data for detecting different malaria parasite clones from different patients and downstream Population genetics analysis. Can I use QIIME or mothur for my data analysis assuming different parasite clones as OTU???
Best regards,
Abe
Hi Abebe
Yes you can, this is a good place to start in any case. I would recommend QIIME :)
Let me know if you have more questions
Best
Ahmed
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