The first part of the queue includes sample submission, login, and initial QC.
When you submit a sample, it is with the understanding that you are ready to go and have done your validation sequencing and workup. Submitting several samples "just to see how they look" is not good practice. You may send them to the Fragment Analyzer service or any other QC you choose ahead of submission. The initial QC is usually a Fragment Analyzer trace, possibly with a Q-PCR or Qubit assay depending on the platform and type of sample you submitted. This procedure usually takes 1-2 BUSINESS days. Once the sample passes QC to our satisfaction, we move to the next step. If it does not pass, you will receive a note with a copy of the trace data. You can then work with us to further process the sample or you can ask for it to be run as-is but without any assurance of quality or output.
The next part of the queue is the time from QC-pass to the start of sequencing.
The wait depends on several factors, including instrument availability, reagent status (if backordered), but most critical is the number of other samples waiting for the same type of run. If you turned in 1 single read 100 sample you might wait longer since we don't get as many of those. Conversely, if you turn in some PE50 samples, you might wait while all the other PE50's ahead of you are run. Samples are run on a first-in first-on basis. Lots of samples ahead of you means a longer wait time. There are 8 lanes on an Illumina HiSeq flow cell. If you are waiting for the HiSeqs, please note that we need 7 samples to start up a run (lane 8 is a requisite control).
The next part of the queue is the time to perform the cluster generation, chemistry, and image each cycle.
This varies by platform (HiSeq vs MiSeq). If your read is longer it will take more time. If you are doing a paired read, add one more business day for the building of the reverse orientation.
The final stages are the pipeline which does the basecalling, and data transfer.
Pipeline and transfer times vary depending on run length, the activity on HPCC (the High Performance Computing Cluster), and other computer phenomena. Some of these factors (such as HPCC down-time or data transfer using other methods like portable hard drives), are beyond our control.