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# System prepended metadata

title: Technologies for whole genome sequencing and de novo assembly

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# Technologies for whole genome sequencing and de novo assembly

> Piotr Mieczkowski, UNC school of medicine

**Short Reads**: Illumina, Ion torrent
**Long Reads**: Pacific Bioscience, Oxford Nanopore
**Optical Mapping**: Bionano Genomics

Quantity application: RNAseq adn ChIPseq
Qualitative: Whole genome assembly, ...


de novo genome assembly



## Chromosome-level genome assembly
### 1. DNA extraction: most important thing is quality of material/DNA
DNA extraction for optimal sequencing results
**circulomics**: high yield, high molecular weigth DNA extraction (simple bind, wash and elute process). Very good if you want to extract large fragments

### 2. Illumina sequencing 

- short read is still more popular (cheaper) than long read sequencing

- Illumina will soon be introducing long read technology (expensive but will be high quality and long reads around 10kb), these long read can be used for scaffolding

- NovaSeq v1.5 reagents and key technology enables: *missed this part*

Why is Illumina so popular? The chemistry

4 nucleotides, each contain a different fluorescent dye, add nucleotides, add them with dye, take picture, strip dye, add more nucleotides, repeat (some work based on 2 channel chemistry with only red and green dyes, each nucleotide has a different color, lack of color, or both)

#### Hi-C (still short read)
 - helps you see chromosome folding
 - different types of Hi-C can serve as advanced chromatin confirmation technologies 

### 3. Long Read Technologies (PacBio and Oxford Nanopore)

- PacBio: Sequel II System - Single Molecule Real Time DNA seq (SMRT): technology allows DNA to loop so polymerase can go around the loop many types producing long, high-fidelity reads 
    - read types: CLR and HiFI long reads
   
- Oxford Nanopore
    - MinION
    - How Nanopore sequencing works: DNA goes through pour with an ion current.
    - read types: long and ultra long reads
    - you can get up to 250kb but important to have high quality DNA (high molecular weight DNA!!)


What type of sequencing is best and what factors to consider:

1. Genome size

Linearize DNA in NanoChannel array (??)
Bionano Access software assembles de novo genome maps







