Best software for amplicon seq data analysis for malaria parasite. Edit
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
I think for this case a suitable approach is to apply the concept of MLST. A recent description in a modified metaMLST at : https://academic.oup.com/nar/article/45/2/e7/2953304/MetaMLST-multi-locus-strain-level-bacterial-typing to use tools normally used with them (eBURST, ). I used Qiime for 16S and for this case you described and if I understood correcly it would also require reference datasets for each of the targeted genes and it would be rather cumbersome to use it in several loci at the same time. Qiime might be used just to separate the kind of genes by using the OTU centroid sequence of each sample included.
you can see
https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fnar%2Farticle%2F45%2F2%2Fe7%2F2953304%2FMetaMLST-multi-locus-strain-level-bacterial-typing
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