Upgrade to Pro
— share decks privately, control downloads, hide ads and more …
Speaker Deck
Features
Speaker Deck
PRO
Sign in
Sign up for free
Search
Search
Illumina
Search
Anton Nekrutenko
February 23, 2021
Education
0
640
Illumina
Intro into Illumina sequencing technology
Anton Nekrutenko
February 23, 2021
Tweet
Share
More Decks by Anton Nekrutenko
See All by Anton Nekrutenko
454
nekrut
3
500
Why academia?
nekrut
0
120
Other NGS Technologies
nekrut
0
2.4k
Spring 2018 | Lecture 1
nekrut
0
1.1k
BMMB554: Genome Conformation
nekrut
0
330
BMMB554: Talks, Papers, Grants
nekrut
0
350
PacBio Applications
nekrut
1
2.4k
NGS Technologies: 454
nekrut
0
2.8k
NGS Technologies: Illumina
nekrut
1
3k
Other Decks in Education
See All in Education
Constructing a Custom TeX Ecosystem for Educational Institutions—Beyond Academic Typesetting
doratex
1
10k
新卒交流ワークショップ
pokotyamu
0
430
Education-JAWS #3 ~教育現場に、AWSのチカラを~
masakiokuda
0
170
より良い学振申請書(DC)を作ろう 2025
luiyoshida
1
3.2k
2025年度春学期 統計学 第4回 データを「分布」で見る (2025. 5. 1)
akiraasano
PRO
0
100
GitHubとAzureを使って開発者になろう
ymd65536
1
120
検索/ディスプレイ/SNS
takenawa
0
6.3k
Case Studies and Course Review - Lecture 12 - Information Visualisation (4019538FNR)
signer
PRO
1
2k
演習問題
takenawa
0
6.3k
SARA Annual Report 2024-25
sara2023
1
180
Design Guidelines and Principles - Lecture 7 - Information Visualisation (4019538FNR)
signer
PRO
0
2.4k
万博非公式マップとFOSS4G
barsaka2
0
280
Featured
See All Featured
Stop Working from a Prison Cell
hatefulcrawdad
270
21k
"I'm Feeling Lucky" - Building Great Search Experiences for Today's Users (#IAC19)
danielanewman
229
22k
Optimising Largest Contentful Paint
csswizardry
37
3.3k
Designing Experiences People Love
moore
142
24k
What’s in a name? Adding method to the madness
productmarketing
PRO
23
3.5k
Building a Modern Day E-commerce SEO Strategy
aleyda
42
7.4k
A designer walks into a library…
pauljervisheath
207
24k
Git: the NoSQL Database
bkeepers
PRO
430
65k
Producing Creativity
orderedlist
PRO
346
40k
Performance Is Good for Brains [We Love Speed 2024]
tammyeverts
10
950
How To Stay Up To Date on Web Technology
chriscoyier
790
250k
A better future with KSS
kneath
239
17k
Transcript
Illumina
Requirements ‣ Reversible termination ‣ Differentiation of nucleotides ‣ Ability
to manipulate on solid support
Preliminary studies
Nucleotides Bentley et al. 2008
Solid support Fedurco et al. 2006
How it works
The overall idea
None
None
None
None
None
None
None
None
None
None
None
Metzker et al. 2010
Extending to paired ends
None
Multiplexin g
Some current stats (2021) illumina.com
Types of Illumina SBS illumina.com
4 channel MiSeq illumina.com
2 channel MiniSeq, NextSeq, NovaSeq illumina.com
1 channel iSeq illumina.com
Platform Number of samples Error rate (%) Median Standard deviation
MiSeq 212 0.473 0.938 MiniSeq 40 0.613 0.459 NextSeq 500 160 0.429 0.827 NextSeq 550 171 0.593 0.435 HiSeq 2500 141 0.112 0.544 NovaSeq 6000 239 0.109 0.350 HiSeq X Ten 163 0.087 0.126 Stoler 2021
How it does not work
Errors
Phasing and Pre-phasing
Illumina chastity filter
Sequence Specific Errors Nakamura et al. 2011
Schematic representation of the (a) inverted repeat and (b) enzyme
preference for the SSE hypothetical mechanistic models. Nakamura K et al. Nucl. Acids Res. 2011;39:e90-e90 © The Author(s) 2011. Published by Oxford University Press.
A typical run Minoche et al. 2011
Coverage as function of GC% Minoche et al. 2011
Low quality bases and alignment Minoche et al. 2011
Goto et al. 2011
Context dependency Minoche et al. 2011
Library prep strategies
TrueSeq PCR-free
Illumina DNA Prep
Illumina Nextera Mate Pair
Illumina Nextera XT
None
Moleculo