This bioinformatics procedure analyses a SARS-CoV-2 sequence to compare it with a range of published primer/probe designs for sequencing and diagnostics assays.
Follow the instructions for Accessing CoV-GLUE on CLIMB to ensure sure you have your own
personal instance of offline CoV-GLUE on CLIMB. You can use either the cov_glue or coguk_cov_glue project installations for this analysis, it does not matter which.
As input, you need to supply consensus FASTA sequences.
From the CLIMB-GLUE server you should be able to access data on the path: /cephfs/covid/
You could copy FASTA files you want to analyse from here to your home directory on this server. Or, you can upload your own data, e.g. using the scp command. You will need to have write access in the directory where these FASTA sequences are located.
This is similar to the functionality available on the CoV-GLUE web application. Start GLUE using gluetools.sh in the the directory containing your FASTA sequence.
Then do:
GLUE> project cov
GLUE> module covPrimerProbeMismatch invoke-function reportSingleFasta <fastaFileName>
This will output an HTML report with the suffix ppReport.html in the same directory as the FASTA file. To quit out of GLUE just use the quit command.
This entry point, only available with offline CoV-GLUE, is more convenient for generating reports for large sets of sequences. Start GLUE using gluetools.sh in the the directory containing your multi-FASTA file.
Then do:
GLUE> project cov
GLUE> module covPrimerProbeMismatch invoke-function reportMultiFasta <fastaFileName>
This will output two tab-delimited text files in the same directory as the FASTA file.
ppReport_summary.txt summarises the number of issues in each sequence.ppReport_issues.txt gives details on each of the detected issues.