speciesprimer
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biologger
Pathovar level
Hi there, Thanks for this great container, very helpful. However, I have some troubles at species and pathovars level.
- I need primers for a particular bacterial species. There are 14 genomes available on NCBI and I know that they are quite different between each other and probably represent two different clusters. Indeed, at the end of the pipeline I get primers that would fit for just one of the two cluster, leaving the second one without primers, as shown by the sequences_details.csv file.
Second issue, pathovar level. I guess the pipeline would also fit at the pathovar level but:
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The first pathovar has only 2 genomes incomplete and It doesn't pass the quality control (even if I said to skip it) becuse there is no gff file (obviously). 28 Jul 2020 08:23:49: > Error 1: 28 Jul 2020 08:23:49: > Error: No .gff files found for QualityControl rRNA
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The second pathovar has the similar name with the first species and thus, the program encounters this synonim and start the species-level primer design.
Thus, I was wondering if I can somehow define the input target sequence by specifing a path or an accession number (and not only the species) to avoid the 1) and 3) issue. (Got no solution for the issue 2). Thanks
