I was very lost in my bioinfomatics comp methods course because I didn't understand what was happening under the hood with the assemblers. Now that I understand the graph theory, everything is starting to flow. Thank you so much for this breakdown. Please continue to post, your videos are saving students who are unfairly paying exorbitant tuition for half assed teaching.
This might be a stupid question, but I am relatively new to metagenomics and aim to fully understand how genome assemblers work. I am wondering why you would want to break up a contig into its k-mers and then find the eulerian path to just to reconstruct the contig again? I think, I might have missed something. Any answer would be appreciated, thank you.
So here comes the indexing part of assembler, many reads might have similar short sequences in between, making k-mers out of reads and than indexing those reads helps in time and memory consumption of an algorithm, coz if we have the information of the index of that k-mer we don't need to reestablish memory for that!
I was very lost in my bioinfomatics comp methods course because I didn't understand what was happening under the hood with the assemblers. Now that I understand the graph theory, everything is starting to flow. Thank you so much for this breakdown. Please continue to post, your videos are saving students who are unfairly paying exorbitant tuition for half assed teaching.
Thank you for sharing the videos. They are not only well explained, but also very interesting.
Great job Loren! Thanks for sharing.
Very clear videos. Thanks a lot!
Great series. Thank you very much
thank you so muh dear.. it helps lot
This might be a stupid question, but I am relatively new to metagenomics and aim to fully understand how genome assemblers work. I am wondering why you would want to break up a contig into its k-mers and then find the eulerian path to just to reconstruct the contig again? I think, I might have missed something. Any answer would be appreciated, thank you.
I mean read, not contig, sorry.
So here comes the indexing part of assembler, many reads might have similar short sequences in between, making k-mers out of reads and than indexing those reads helps in time and memory consumption of an algorithm, coz if we have the information of the index of that k-mer we don't need to reestablish memory for that!