Hi,
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!
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!