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Lecture Notes 4/6/2015
Note Taker: Christopher Kan
A road map to the Denovo-Assembly of the Banana Slug Genome
Denovo VS. Reference Genome
Scaffolds and Contigs
○ You sum the size of the scaffolds or contigs until you reach 1/2 the linear length of a genome. The size of the last constituent part of the N50. It’s a way to obtain a median-esque measure of assembly quality
Definition: Kmer - Short unique element of DNA of a certain length n
A priori knowledge of a genome
§ Some have low variation and high synteny - Birds
Sequencing Technology
○ Sanger
§ It took me a long time to understand how this works these two video helped me: Link
§ Problems
~ Need to wash with low concentration to ensure most cells only have one molocule
~ Random. This property used to error correct
~ Molocule held by molocule that clips off one nucleotide at a time - exonuclease
~ Measure the charge at the nanopore. * OR sequence the molocule as it goes through as its held with an helicase * Some systematic errors - Harder to correct * Can use a hair pin to run both side of DNA so its effectiely paired * No restriction on size hypothetically
Issues with 3rd Gen
Note Taker: XXX
Discussion
Posted notes and link to youtube videos - CK