Variant Calling With Long Vs Short Reads
38 sec. read
The basic steps in a variant-calling workflow based on mapping short reads to reference genomes are so established in my mind that when I finally got to play with our nanopore sequencer, it took me about a week of fiddling* to realize that mapping long reads doesn’t proceed in quite the same way.
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.