User Notes On Bacterial Haplotype Reconstruction Software

4 min. read

About 10 months ago, armed with short-read sequences of experimentally evolved bacterial and archaeal populations, I decided that it would be “easier” to use haplotype reconstruction software to recover genotypes, than to either eyeball population-level variant frequencies over time (planning to write a paper on this - will link when it’s in preprint), and then logically deduce which variants occurred on the same genetic background, or to sample genotypes from the population by selecting a number of clonal isolates for whole genome sequencing (planning a blog post on how to determine the number of isolates to appropriately sample a population with given amount of genetic diversity). I wasn’t confident that I could do the former in a coherent, reproducible way, and in rejecting the latter, I was trying to avoid more lab work and sequencing costs.

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