While they are both currently supported, BCL Convert is illuminas plan to replace bcl2fastq. BCL Convert is supposedly faster, I've seen users report 25-100% speed increases. It was lacking a lot of features when it was released but it looks like most features available to bcl2fastq are now available to BCL Convert as well.
However, I have also seen that it makes significant changes to the structure of the run directory and the files produced. If you run an automated pipeline this would likely mean there is a good amount of additional work required to transition.
Some things I'd be interested in hearing from you all are:
- Have you made the switch? Why / Why not?
- If you did make the switch, have you had any issues with missing features / bugs?
- If you did make the switch, what kind of performance gains did you see?
Thank you, I would like to clarify the part about nextseq 1000/2000 only supporting bcl-convert. On illumina's site here it says that both bcl-convert and bcl2fastq are supported?
I have not been able to find anything about the novaseq x and whether it will be supporting both or not and was wondering where you have seen that any new sequencer coming down the pipe will not support bcl2fastq?
Kevin : When we acquired NS 2K I could swear that bcl2fastq was indicated as not supporting NS 2K, so that was the reason we ended up setting up a separate workflow for it with
bcl-convert
. Your link above seems to now indicate that is not the case but at this point that is water under the bridge.bcl-convert
is "smarter" about dual-indexed workflows and how it detects if i5 needs to be RC'ed or not. So there are some advantages but if you have been usingbcl2fastq
for a long time then you may miss its flexibility with command line parameters.Like I said above if you foresee continuing to do Illumina sequencing in future then it would be prudent to at least start planning for the switch to
bcl-convert
.