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I am comparing Illumina MiSeq (using MiSeq v3 kit) and MiniSeq (MiniSeq High Output kit) instruments for sequencing E.coli and Salmonella. I am curious if there is any way to bioinformatically distinguish between the sequences generated by these instruments without the header information? Would it simply be the read length difference (MiSeq=2 x 300bp vs MiniSeq=2 x 150 bp) and output (MiSeq=13.2-15Gb vs MiniSeq=6.6-7.5Gb). Quality wise they look nearly identical in my experience. Thank you.

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    $\begingroup$ Can you explain why? I mean, why would you need this? Presumably, you know what sequencer you used, right? And if not, you can use the header. Why would you need to hobble yourself this way? And why aren't the differences you listed (one produces reads of twice the length and files of twice the size of the other) already enough? What else are you looking for? $\endgroup$
    – terdon
    Commented Feb 21 at 14:22
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Feb 21 at 16:06
  • $\begingroup$ Why could you possibly need this?? MiSeq is higher throughput so you should have more reads under certain assumptions $\endgroup$ Commented Feb 22 at 21:31

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