Ghi hic icd abc bcd fgh cde def efg fgk gkl de bruijn

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Unformatted text preview: raph of a Genome Example GGenome: AABCDEFGHICDEFGKL Example enome: BCDEFGHICDEFGKL ! ­mers ABCD BCDE CDEF DEFG EFGH GHIC HICD ICDE EFGK FGKL (!−1) ­mers ABC BCD CDE DEF EFG GHI HIC ICD FGK GKL De Bruijn Graph of a Genome EExample Genome: AABCDEFGHICDEFGKL xample Genome: BCDEFGHICDEFGKL GHI HIC ICD ABC BCD FGH CDE DEF EFG FGK GKL De Bruijn Graph of a Genome Bulges (undirected cycles) and whirls (directed cycles) Example Genome: ABCDEFGHICDEFGKL occur because of sequencing errors or repeats in the genome. GHI HIC ICD ABC BCD FGH CDE DEF EFG FGK GKL De Bruijn Graph of a Genome Example GGenome: AABCDEFGHICDEFGKL Example enome: BCDEFGHICDEFGKL GHI HIC 2 ICD ABC BCD 1 FGH CDE DEF EFG FGK 3 GKL Typical De Bruijn Graph However, this is over a billion ver2ces (for a very small bacteria genome). … De Bruijn Graph of a Genome Example GGenome: AABCDEFGHICDEFGKL Example enome: BCDEFGHICDEFGKL GHI HIC 2 ICD ABC BCD 1 FGH CDE DEF EFG FGK 3 GKL De Bruijn Graph of a Genome EExample Genome: AABCDEFGHICDEFGKL xample Genome: BCDEFGHICDEFGKL ABC BCD CDE DEF EFG FGK GKL De Bruijn Graph of a Genome Example GErroneous Genome: CDEFGKL KL Resul2ng enome: ABCDEFGHI ABCDEFG ABC BCD 1 CDE DEF EFG FGK GKL Paired ­end Reads •  Random fragment with an approximately known size. •  Both ends are sequenced. •  Specified prior to data acquisi2on. ACTATAAT Insert Size ACCGCGAT Coverage Standard (Mul2 ­cell) Data (Chitsaz et al., 2011) Coverage Coverage Single ­cell Data (Chitsaz et al., 2011) Detangling the de Bruijn Graph Even using mate ­pair informa2on, the de Bruijn graph is highly tangled. There are the following op2ons for detangling the de Bruijn graph: 1.  Error correc2on of reads. 2.  Bulge and whirl removal. 32 Detangling the de Bruijn Graph Even using mate...
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