We are wanting to do a pathogenomic study of some E coli strains. The idea is basically to compare the genome of these strains between them and against reference genomes and analyse them for virulence factors.
Among local NGS service providers I found these two options: either Illumina Hiseq2000, paired-ends, or 454. The 454 provider says the expected coverage is about x11-17. I wonder if it is too low? But it also provides a more complete analysis of genomes then the first provider (I'm an "end user", not a bioinformatics expert). The problem of course is cost: 454 is 3 times more expensive.
Any suggestions or ideas? Anyone dealing with a similiar project that would like to share a bit of his experience?
Thanks to all and have a nice day
Among local NGS service providers I found these two options: either Illumina Hiseq2000, paired-ends, or 454. The 454 provider says the expected coverage is about x11-17. I wonder if it is too low? But it also provides a more complete analysis of genomes then the first provider (I'm an "end user", not a bioinformatics expert). The problem of course is cost: 454 is 3 times more expensive.
Any suggestions or ideas? Anyone dealing with a similiar project that would like to share a bit of his experience?
Thanks to all and have a nice day
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