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So, I'm working with a several bacterial genomes, and I'm learning bioinformatics as I work, so forgive me if this is a dumb question. My genomes have a lot of repeat sequences (for a prokaryotic genome) that are really the last elements to place into the genome, however I want to make sure that I assemble everything correctly. Thus, my question is how do you make sure that repeat sequences are placed correctly in the genome. Is the best way to PCR out from the repeat sequences and see where the different sequences belong, or are there other easier and quicker ways to accomplish this goal. Basically, what is the fastest and most accurate way to determine the location of the repeat sequences. Sorry again if this is an dumb question, but I don't know that much about genome sequencing and bioinformatics and I'm having to learn a lot from everyone here. Thanks
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Last edited by clostridium40; 09-02-2011, 01:25 PM.
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM