Any idea if there's a way to get the Instrument type (i.e. NextSeq, HiSeq, etc), from the instrument name field in the Fastq read header? - I've tried looking for a map of sorts in Illumina's documentation, but to no avail.
There was a post @SeqAnswers where we had a recap of the types of sequencer specific fastq headers (my google-fu has not turned up that post yet). Following is a very rough approximation of start of fastq headers that are sequencer specific.
Edit: Just want to add that it is possible to change the default read header in one of the set up files (so the following may not always be true).
Illumina provided the following information regarding FCID mapping to instruments. The indicated characters are the last four of the nine-character FCID (excepting MiSeq). Please note that this is not comprehensive and there may be new additions in the future.
I believe you can extract the instrument type from the FCID in the read identifier (e.g. our HiSeq FCIDs all end in 'ACXX', MiSeqs all start with 'MS'), but you may need to contact Illumina to determine the complete code.