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Hello all,
I am a grad student at Texas Tech University and I have been tasked with reporting SNPs between 2 Listeria (bacteria) strains that were isolated 6+ years apart. We are trying to show genetic evolution of the strains. I had tried to run kSNP, but was told that I needed a different SNP calling program than that. I was told to look for a "Reference based" and a "Graph or Map based" calling programs, and to run both programs and compare the results.
I am very much a newbie at this so any help and recommendations on which programs to use would be very much appreciated.
The genomes were sequenced on the Miseq and assembled using A5
Thanks in advance
I am a grad student at Texas Tech University and I have been tasked with reporting SNPs between 2 Listeria (bacteria) strains that were isolated 6+ years apart. We are trying to show genetic evolution of the strains. I had tried to run kSNP, but was told that I needed a different SNP calling program than that. I was told to look for a "Reference based" and a "Graph or Map based" calling programs, and to run both programs and compare the results.
I am very much a newbie at this so any help and recommendations on which programs to use would be very much appreciated.
The genomes were sequenced on the Miseq and assembled using A5
Thanks in advance