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  • Suitable method for genome assembly using short reads

    Which illumina sequencing platform is more suitable for de novo genome assembly for genome size of 500Mb.?
    Illumina HiSeq or Novaseq6000?


  • #2
    Hey,

    I have a personal preference towards the NovaSeq because I used to work on one and heard coworkers who have previously used the HiSeq complain about some issues they've experienced. I don't know that this is true, but the NovaSeq has different flow cell options which allow you to obtain as many reads as you like.

    The only negative aspect about the NovaSeq that I'm aware of, is that people have issues sequencing G heavy regions since it is a 2-channel sequencer.

    Do you have access to your own machines or were you going to have the samples sent off somewhere? Also, do you know the number of reads and coverage you need for your experiment?


    Here's a paper where they compared data from several sequencers that may also be useful to you.
    https://academic.oup.com/nargab/arti...qab019/6193612

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