Hello,
I wish to sequence the genomes of approx. 70 Clostridium perfringens strains for bioinformatic analyses. I was hesitating between 2 Illumina technologies: MiSeq and Hiseq. Could you help me to find which one is more appropriated and efficient?
Thank you a lot for your answers!
Regards,
Nicolas
Hi Nicolas,
Miseq reads output passing filter are 50 M using v3 cartridge. So you will need to run 15 strain of Clostridium each time ( 3 MB each strain) for 70 you need 5 runs in Miseq. In Hiseq you probably do in one run All 70. That’s the difference.
I would consider using PacBio in circular consensus sequencing (CCS) mode. The assembly of genomes is likely to work out in one sweep; I had very good experience with this type of sequencing for Streptomyces spp. (see Serrano et al. 2019; DOI: 10.1128/MRA.00355-19).
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Which kind of bioinformatics analysis are you willing to analyse? It important to mention them since one technology or other would improve much the quality of your sequence and therefore your analysis. I would go for dual sequencing as Illumina and PacBio if you want to screen for new transcripts or transcripts coming from different TSSs (transcription starting sites) or combination of expression between different promotors. Your aim should be a hint for the best platform.
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