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
DBG-Assemble A Genome
Search
Buttonwood
August 28, 2013
Education
0
22
DBG-Assemble A Genome
Assemble a genome
Buttonwood
August 28, 2013
Tweet
Share
Other Decks in Education
See All in Education
Human-AI Interaction - Lecture 11 - Next Generation User Interfaces (4018166FNR)
signer
PRO
0
530
Técnicas y Tecnología para la Investigación Neurocientífica en el Neuromanagement
jvpcubias
0
130
学びは趣味の延長線
ohmori_yusuke
0
110
日本の情報系社会人院生のリアル -JAIST 修士編-
yurikomium
1
120
Test-NUTMEG紹介スライド
mugiiicha
0
160
中間活動報告会 人材育成WG・技術サブWG / 20250808-oidfj-eduWG-techSWG
oidfj
0
650
ARアプリを活用した防災まち歩きデータ作成ハンズオン
nro2daisuke
0
180
AI for Learning
fonylew
0
180
RSJ2025 ランチョンセミナー 一歩ずつ世界へ:学生・若手研究者のための等身大の国際化の始め方
t_inamura
0
280
Common STIs in London: Symptoms, Risks & Prevention
medicaldental
0
140
情報科学類で学べる専門科目38選
momeemt
0
590
Transición del Management al Neuromanagement
jvpcubias
0
210
Featured
See All Featured
Faster Mobile Websites
deanohume
309
31k
Thoughts on Productivity
jonyablonski
70
4.8k
Sharpening the Axe: The Primacy of Toolmaking
bcantrill
44
2.5k
Mobile First: as difficult as doing things right
swwweet
224
9.9k
The Pragmatic Product Professional
lauravandoore
36
6.9k
Distributed Sagas: A Protocol for Coordinating Microservices
caitiem20
333
22k
Dealing with People You Can't Stand - Big Design 2015
cassininazir
367
27k
A designer walks into a library…
pauljervisheath
207
24k
[RailsConf 2023] Rails as a piece of cake
palkan
57
5.8k
Site-Speed That Sticks
csswizardry
10
820
CoffeeScript is Beautiful & I Never Want to Write Plain JavaScript Again
sstephenson
162
15k
The Art of Delivering Value - GDevCon NA Keynote
reverentgeek
15
1.7k
Transcript
De Bruijn Graph
[email protected]
http://buttonwood.github.io
Origin of de Bruijn graphs Graph Theory: Hamilton path VS
Euler path In 1946, the Dutch mathematician Nicolaas de Bruijn The ‘superstring problem’: find a shortest circular ‘superstring’ that contains all possible ‘substrings’ of length k (k-mers) over a given alphabet.{0,1} -> {A,T,C,G}
De Bruijn Graph of a Small Sequence
Let’s go!From simple examples...
Double-Stranded Nature of Genome ATGGAAGTCGCTTCCAT TACCTTCAGCCAAGGTA 5’ 5’ 3’ 3’
Impact of Changing k-mer Size Big? Small? Avoid even k?
avoid even k, because with even k, many k-mers become reverse comcomplements of their own sequences.
DBG OF A GENOME
Sequencing errors ---> Tips A B C D • Clip
the short tips that had lengths < 2 Kmers • Or less number of reads through it.
Sequencing errors ---> CrossLink ATGGAAGTCGCG ATGGAAG TGGAAGT GGAAGTC GAAGTCG AAGTCGC
AGTCGCG GAGGAAGACCTT GAGGAAG AGGAAGA GGAAGAC GAAGACC AAGACCT AGACCTT GAGGAAGTCC AGGAAGT ATGGAAGTCG seq1 seq1-read1 seq2-read1 seq2 • Remove low-coverage nodes. Low-coverage connection
Sequencing errors --->Bubbles ATGGAAGTCGCG... ATGGAAG TGGAAGT GGAAGTC GAAGTCG AAGTCGC AGTCGCG
TGGAAGA GGAAGAC GAAGACG AAGACGC AGACGCG ATGGAAGACG... ATGGAAGTCG... seq1 seq1-read1 seq1-read2 • Remove low-coverage paths. • Same as SNP Bubbles. Low-coverage paths Bubbles
Repetitive Regions Simple Repeats Tandem Repeats
TINY OR LONG REPEAT ATTTAAATTAGCGATATTAGCATCTCTT .... AATTA ATTAG TAGCG AGCGA
GCGAT CGATA GATAT ATATT TATTA TAGCA AGCAT GCATC CATCT ATCTC TCTCT ... TTAGC c a d b e .... AATTAGC ATTAGCG TAGCGAT AGCGATA GCGATAT CGATATT GATATTA ATATTAG TATTAGC TTAGCGA ATTAGCA TTAGCAT TAGCATC .... You see what? Bigger k-mer(long overlap) cross the repeat.
Haplotype Differences
SNPs--->Bubbles ATGGAAGTCGCG... ATGGAAG TGGAAGT GGAAGTC GAAGTCG AAGTCGC AGTCGCG TGGAAGA GGAAGAC
GAAGACG AAGACGC AGACGCG ATGGAAGACG... ATGGAAGTCG... hap1 hap1-read1 hap2-read1 • Equal coverage paths. Equal-coverage paths Bubbles ATGGAAGACGCG... hap2 ? Adjacent SNPs ATGGTAGTCGCG... ATGGAAGACGCG... hap1 hap2
Indels--->Bubbles ATGGAAGTCGCGTCGA... ATGGAAG TGGAAGT ... CGCGTCG GCGTCGA TGGAAGG ... GGCCTCG
ATGGAAG---- GCGTC... ATGGAAGTCG... hap1 hap1-read1 hap2-read1 • Equal coverage paths. • Long road map. Equal-coverage paths Bubbles ATGGAAG-----GCGTCGA... hap2 ? Adjacent SNPs with Indels ATGGTAGTCGCAAGCC... ... ATGGAAGACGC---GCG... hap1 hap2
ASSIGNMENT 1 Let Kmer=4 Let Kmer=5 Let Kmer=7 ATTA TTAG
TAGG AGGA ATTAGGATCATGATCCTCTGTGGATAAGATCTTTTTATTTAAAGATCTCTTTATTAGATCTCTT … ATTA DBG of Genome; DBG of Reads; L = 15 TRY!
ASSIGNMENT 2 Simulated Hap1 about 1M: Count K-mer freq; Then
sequence 40X; Then add repeat/Error rate; Then SNPs(two haplotype);