BIoinfor02

Bioinformatika Lanjutan

Grup A: Sequencing Method

Whole Genome Sequencing Methods

Top 3 dalam RefSeq database?

1. Illumina

2. PacBio

3. Roche-454
   
   (Segerman, 2020)

Whole Genome Sequencing Methods

Tren saat ini...?

1. Illumina

2. PacBio

3. Nanopore 📈

4. Roche-454 📉
   (Segerman, 2020)

Multiple Choice

Output dari proses sekuensing disebut...

• Reads

• Contigs

• Scaffold

• Amplicon

Input, Proses, Output

Input: DNA
Proses: Basecalling
Output: Reads

Multiple Select

Kualitas hasil sequencing dilihat dari...

• Phred Score

• Read depth

• Discriminatory Power

Phred Score

Q = -10log (Peluang Kesalahan).

Q30 berarti ada kemungkinan 1 banding 1000 ada kesalahan pada basa tsb.
Setiap basa pada hasil sequencing memiliki Phred Score



(Tassios & Moran-Gilad, 2018)

FASTQC

PacBio
Nanopore

>1 kb

Long Reads

Illumina

150-250 bp

Short Reads

Read types

Short vs Long Reads

Analogi main puzzle dengan kepingan kecil vs besar

Poll

Lebih sulit mana untuk menghasilkan gambar utuh?

• Kepingan Besar

• Kepingan Kecil

• Sama saja

Coverage/Depth

References

Segerman, B. (2020). The most frequently used sequencing technologies and assembly methods in different time segments of the bacterial surveillance and refseq genome databases. Frontiers in Cellular and Infection Microbiology, 10, 527102. https://doi.org/10.3389/fcimb.2020.527102

Tassios, P. T., & Moran-Gilad, J. (2018). Bacterial next generation sequencing (Ngs) made easy. Clinical Microbiology and Infection, 24(4), 332–334. https://doi.org/10.1016/j.cmi.2018.03.001