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GS Junior amplicon sequencing - analysis tools



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  • GS Junior amplicon sequencing - analysis tools


    could anyone recommend an open-source analysis pipeline for GS jr. amplicon data?
    I found VIP for variant identification, but the download page was invalid meanwhile.
    I have no access to Roche tools. So which would be the appropriate steps for variant analysis? I have read the following so far:

    1. split .fna files (+/- strand) --> how/why?
    2. trim Roche adaptors
    3. BLAT or STAR against reference amplicon/genome?

    Many thanks in advance!

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