speciesprimer
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biologger
The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
Hi, I am having the following issue. Any help will be appreciated. A problem with the BLAST results file /primerdesign/Lactobacillus_curvatus/Pangenome/results/primer/primerblast/primer_0_results.xml was detected. Please check if the file was removed and...
Hi Matt, Thank you for your great program! I noticed that multi-copy genes were screened out during the design process ''' .... core genes: 1709 _**single copy core genes: 1371**_...
Hi, When I run or rerun speciesprimer (on a docker container with 15.51 gb RAM allocated to it) a single results file is not successfully created. I can not determine...
Hi, I am trying to download the blast_db and keep getting the following md5 error using both the html and from the command line. Any ideas please? thanks Downloading...nt.00.tar.gz 100%...
Dear, I am interested in design primers for some serovars of Salmonella enterica with your pipeline. Is possible to use it in this case? Thank you
Hi, I've been able to get this nice tool running for my project but one thing I have consistently noticed is that the final *primer.csv file has `Probe` columns always...
Hello, I had tried to install SpeciesPrimer with rootless docker, and it gave me the following issue: docker: failed to register layer: ApplyLayer exit status 1 stdout: stderr: lchown /root/.cpanm/work/1574351743.6/Number-Compare-0.03:...
core genes: 2017 single copy core genes: 1836 Number of conserved sequences: 1812 species specific conserved sequences: 536 potential primer pair(s): 4578 primer pairs with good target binding: 4260 primer...
Any plans on creating a conda recipe for those that would like to integrate speciesprimer into a data analysis environment with other software?
It would be great if the list of good target binding primers would be in the output even if there are 0 primer pairs passing non-target PCR check. In the...
