De Bruijn graph toy example in Fastg format

gistfile1.txt

De Bruijn graph toy example

Genome:
ATGAAGTGGGTAAC

Reads:
ATGAAGTGGG
   TAGTGGGTAA
    AGTGCGTAAC

K-mers:
1 ATGA
2  TGAA
3   GAAG
4    AAGT
5    TAGT
6     AGTG
7      GTGG
8       TGGG
9        GGGT
10        GGTA
11     GTGC
12      TGCG
13       GCGT
14        CGTA
15         GTAA
16          TAAC 
          

>km1:km2;
ATGA
>km2:km3;
A
>km3:km4;
G
>km4:km6;
T
>km5:km6;
TAGT
>km6:km7,km11;
G
>km7:km8;
G
>km8:km9;
G
>km9:km10;
T
>km10:km15;
A
>km11:km12;
C
>km12:km13;
G
>km13:km14;
T
>km14:km15;
A
>km15:km16;
A
>km16
C


If we create contigs in the de Bruijn graph we can compress this into
>c1:c3;
ATGAAGT
>c2:c3;
TAGT
>c3:c4,c5;
G
>c4:c6;
GGTA
>c5:c6;
CGTA
>c6;
AC

Recognizing the bubble in the middle this can be reduced to
>c1:c3;
ATGAAGT
>c2:c3;
TAGT
>c3;
G[1:alt|G,C]GGTAAC


And finally
>c1;
ATGAA[1:alt|A,T]GTG[1:alt|G,C]GGTAAC