We got a Nextseq, and as the local person who has the duty of running our Hiseq/Miseq "primary analysis pipeline", I am trying to get everything set up with our current analysis pipeline and in-house lims.
I would like to collect any tips anyone has for transition to Nextseq somewhere. So far, I know that I need bcl2fastq version 2, which comes with a user guide. This appears to be a binary as opposed to the previous standalone bcl2fastq, which was a perl script that generated a shell script and the options are slightly different.
I have heard tell of picard breaking on nextseq data.
Is anyone using basespace? Illumina seems to be pushing it especially for the nextseq, but there are a few limitations that are holding us back (we use a lot of non-human-mouse-rat genomes, individual user accounts with no notion of "labs" or "groups" of any kind seem kinda weird).