I have a bacteria on lab and have its reference genome so what would be the best coverage for "total length (Mb): 4.21561" of a bacterial genome sequenceing? and hiseq or miseq?
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Clark_BioMorgan •
That depends on desired or possible read length, downstream application (why sequence it) and repetitive content of the genome.
I would like to do whole genome sequencing (4,000,000bp) of a bacteria which has a reference sequence. so I won't do de novo assembly I will do reference based assembly. So what is your opinion?
MiSeq should be sufficient to cover a genome like that, MiSeq V3 has ~45M 300bp paired-end reads (depending on cluster density). Just rough calculation: 40 million reads of 300bp => 3000 fold coverage which is an enormous/outrageous over sequencing. You definitely don't need HiSeq for this, but offcourse it depends on what machines you have available and/or the prices of your sequencing provider.
Since your genome is haploid about 5-15 fold coverage should be fine for calling SNPs...
Try Illumina's sequencing coverage calculator.
Tried it. But they actually ask the coverage to me so I don't really understand why :)
Since you have a reference available coverage you want would depend on what you are trying to do as @decosterwouter said above.
If you are looking to call SNP's (or do rearrangement analysis) then 5-10x coverage may be enough. If your strain turns out to differ significantly from the reference (and many strains might depending on how long they have been cultured/in use in your lab) you may need to assemble a new reference for your strain.
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