Mark as Pass/Fail
When sequencing results are not high enough quality to produce a satisfactory consensus sequence then you can mark the sequencing reaction in the LIMS as failed so that they can be re-run. Conversely they can be marked as passed so that administrators know that sequencing was a success and a consensus sequence is available. Marking as pass/fail can be done at any step throughout the assembly pipeline, and this wiki will mention when the best times are to do so.
To mark as pass or fail, select the appropriate reads, contigs or alignments and go to Biocode > Mark as Pass in LIMS or Mark as Fail in LIMS.
If you imported your traces directly from disk, rather than from a plate in the LIMS, you can attach the traces to the plate as part of the mark operation by turning on "Add chromatograms to LIMS". This saves the original raw trace which excludes any editing and trimming. If you selected contigs for marking then you will also be asked for the type of consensus sequence to use. The consensus sequence is covered in more detail under Viewing and Editing Contigs.
After marking as pass or fail you can see the outcomes on the appropriate cycle sequencing plates in the LIMS database (refer to the LIMS documentation). Passed wells are marked green while fails are red. Marking as pass/fail also records in the LIMS the consensus sequence and some of the options used to reach that consensus. These sequences will be available in LIMS searches as "Sequences".