Searching tips to effectively sequence poor quality/quantity bacterial DNA using Miseq NGS. One of my earlier experiment involving starting concentration of 165ng/mL of bacterial DNA yielded an average of
There has been success sequencing genomes with extremely low amounts of DNA
Article Validation of picogram- and femtogram-input DNA libraries fo...
I wonder why do you want to sequence a low quality DNA? Did you try all kind of kits/methods for genomic DNA extraction? As far as I know its quite simple in Bacteria at least if you run extracting DNA from very special cultures conditions and the grow is quite poor but the DNA quality should even be improved with kits.
If you have gotten sequence back at 5x coverage, you should just be able to increase the proportion of that library in the pool when sequencing to get a higher coverage. If using NexeraXT library preps, the input you have is very close to what they recommend as a starting input
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