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:
If you have/plan to acquire a NextSeq 1000/2000 (and any new sequencer that is going to come down the pipe) then you have no option but to use bcl-convert. Illumina does not support using bcl2fastq with new sequencers. If you can use DRAGEN included in NextSeq then much of work can be done there itself. There is no separate license required to use DRAGEN on NextSeq 1/2000 now.
If you run an automated pipeline this would likely mean there is a good amount of additional work required to transition.
Yes you will have to make changes to your own software/processes. Samplesheet formats are subtly different, if you generate them programmatically. A number of command line options in bcl2fastq have been transferred to SampleSheet directives in bcl-convert. If you parse the demux reports from HTML files in bcl2fastq then they have been moved to comma separated files in bcl-convert and there are some changes to way the number of reads are accounted for. Top undetermined indexes found in the pool are now reported in a separate file and so on.You would need to do the work necessary to accommodate these changes at some point. If you are in the Illumina sequencing business then it would be better to start now then later.
bcl-convert fully supports all sequencers so it is backwards compatible. A nice summary of differences is available from Illumina. We have not specifically checked for or worried about performance gains.
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 using bcl2fastq 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.
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