I am new in NGS. For my research I need to choose a technique between MiSeq and HiSeq. I have 100 mouse fecal samples. I was planning to do the MiSeq but it's not fast as HiSeq. On the other hand HiSeq is much expensive than MiSeq. So, I wanted to know which one would be better in terms of reads, coverage and overall good quality result.
As you have already pointed out, it depends on how much you're willing to spend? Of course, HiSeq is better in terms of technicalities and throughput but you'll have higher cost down the road. In my opinion, with 100 samples, MiSeq is good enough with better chemistry solutions nowadays, you can get good quality and length at a lower price (of a MiSeq). At the end of the day, what you need is a good data from good quality samples.
One important thing you did not mention what you want to analyse or what is your amplicon lengths? The choice of sequencing platform would depend much on the purpose than the speed of sequencing. I would consider the speed of sequencing the least important factor to choose from them. Moreover, the read length, depth and quality has limitations towards the sample side than sequencing platform. Both platforms works well for specific needs. Concludingly, purpose should be defined prior to choose among the sequencing technology.
When you say 'microbiome' sequencing, you mean 16S amplicons (aka microbiota) or metagenome ? For 16S amplicons (especially V4 region) MiSeq will be just fine. But for metagenomics or regions longer than V4, you would wanna go to HiSeq.
Thanks for the answers. I am using V3-V4 region. So, the amplicon length is 428bp. Can you tell me the desired coverage for MiSeq? I am confused in the coverage area too.
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