Hello SEQanswers community!
I'm new to the forum but have already gained a lot of insight into some of the data analysis platforms that I might consider using for my research!
I'm a classical bacteriologist at the University of Saskatchewan and am just starting a project where we are planning on using the MiSeq Illumina system to sequence the genomes of a collection (~50 isolates) of bacteria collected over about 10 years. The idea behind the project is essentially to use whole genome sequencing as a replacement for older DNA fingerprinting techniques like MLST and PFGE. Our goal is to compare the 'DNA fingerprint' with clinical epidemiological data and also look for temporal trends. Essentially we would like to draw a meaningful tree and see if the branches correspond to any of our epidemiological data. We aren't planning on closing all the gaps between the contigs and are hoping to do the analysis on draft genomes.
I have been doing a lot of reading and it looks like MUMmer might be the program that I should consider using. As someone who is new to the NGS world, without any linux experience, I'm finding it difficult to design an in-silico workflow. I know that there's a lot of home brew out there when it comes to bioinformatics and I don't want to fall into any newby traps
! So far we haven't done any of the sequencing, and I'm not planning on starting until I have a better idea of what I'm going to do on the bio-informatics end.
If anyone knows of any similar studies that have been done with well described bioinformatics M&M, or can point me towards a reference textbook or bio-informatics paper that could help me come up with a more detailed plan I would be very appreciative!
I'm new to the forum but have already gained a lot of insight into some of the data analysis platforms that I might consider using for my research!
I'm a classical bacteriologist at the University of Saskatchewan and am just starting a project where we are planning on using the MiSeq Illumina system to sequence the genomes of a collection (~50 isolates) of bacteria collected over about 10 years. The idea behind the project is essentially to use whole genome sequencing as a replacement for older DNA fingerprinting techniques like MLST and PFGE. Our goal is to compare the 'DNA fingerprint' with clinical epidemiological data and also look for temporal trends. Essentially we would like to draw a meaningful tree and see if the branches correspond to any of our epidemiological data. We aren't planning on closing all the gaps between the contigs and are hoping to do the analysis on draft genomes.
I have been doing a lot of reading and it looks like MUMmer might be the program that I should consider using. As someone who is new to the NGS world, without any linux experience, I'm finding it difficult to design an in-silico workflow. I know that there's a lot of home brew out there when it comes to bioinformatics and I don't want to fall into any newby traps
! So far we haven't done any of the sequencing, and I'm not planning on starting until I have a better idea of what I'm going to do on the bio-informatics end.If anyone knows of any similar studies that have been done with well described bioinformatics M&M, or can point me towards a reference textbook or bio-informatics paper that could help me come up with a more detailed plan I would be very appreciative!
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