DBG-Assemble A Genome

Transcript

1. De Bruijn Graph tanhao2013@gmail.com http://buttonwood.github.io

2. 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}

3. De Bruijn Graph of a Small Sequence

4. Let’s go！From simple examples...

5. Double-Stranded Nature of Genome ATGGAAGTCGCTTCCAT TACCTTCAGCCAAGGTA 5’ 5’ 3’ 3’

6. 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.

7. DBG OF A GENOME

8. Sequencing errors ---> Tips A B C D • Clip

   the short tips that had lengths < 2 Kmers • Or less number of reads through it.

9. 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

10. 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

11. Repetitive Regions Simple Repeats Tandem Repeats

12. 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.

13. Haplotype Differences

14. 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

15. 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

16. 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!

17. ASSIGNMENT 2 Simulated Hap1 about 1M: Count K-mer freq; Then

    sequence 40X; Then add repeat/Error rate; Then SNPs(two haplotype);