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  • Reconstructing a de Bruijn Graph from Velvet's LastGraph

    Hi,

    I was wondering if someone can explain/ give hints to me about how to regain a de Bruijn Graph from Velvet's LastGraph representation of nodes and arcs?

    I created an example with hashsize (k)=7 and told velvetg to "keep all data" by setting cov_cutoff=1 min_contig_lgth=1:

    Code:
    >SEQUENCE_0
    TTTTTTCATGCATGCTAGCGTGTGTGTGT
    >SEQUENCE_1
    GTGTGTGTGTTAGCTGCAGTATGCGGAAC
    >SEQUENCE_2
    ACACACACACATCGATTGTTATGCGGAAC
    >SEQUENCE_3
    TATGCGGAACGCATTGCTAACTCGGGGGG
    results in

    Code:
    5	4	7	1
    NODE	1	12	13	13	0	0
    GCTAGCATGCAT
    GCTAGCGTGTGT
    NODE	2	1	6	6	0	0
    G
    C
    NODE	3	1	7	7	0	0
    T
    A
    NODE	4	15	15	15	0	0
    TAGCTGCAGTATGCG
    CTGCAGCTAACACAC
    NODE	5	14	14	14	0	0
    TCGATTGTTATGCG
    ACAATCGATGTGTG
    ARC	1	-1	2
    ARC	-1	2	1
    ARC	2	3	6
    ARC	-2	-3	4
    ARC	3	4	1
    ARC	-3	5	1
    I don't get exactly HOW to read out the sequence from the traversal of the nodes, e.g. (1) --> (-1), (-1) --> (2) and so on.
    Once I know how to read the sequence I could rebuild a simple de Bruijn Graph from it. Or is there maybe some simpler (back-)transformation from LastGraph to de Bruijn Graph?

    The (very old) manual page of Velvet is not helping too much

    Any help highly appreciated.

    Thanks!


    ------------------------------
    EDIT
    ------------------------------

    Another example:
    Let's take a sequence s=ACTGGACTGAA
    As I recall this results in the dBG of s:
    Code:
    ACT --> CTG --> TGG --> GGA --> GAC --> (ACT...)
             | 
             |--> TGA --> GAA
    Velvet's result is (k=3, velvetg cov_cutoff=1 min_contig_lgth=1):
    1 1 3 1
    NODE 1 5 7 7 0 0
    TGGAC
    CCAGT
    ARC 1 1 1

    This means I would be able to recover:
    Code:
    (Node 1 upper seq.)              TGGAC
                                     |||    --> ACTGGAC  (and an arbitrary amount of concatenations of this seq. since ARC (1) --> (1) )
    (Node 1 lower seq. rev.comp.)  ACTGG
    BUT, it seems to me that Velvet is missing the entire alternative path "TGAA" of the dBG of s.
    I would have expected another node and an additional arc to find that sequence.

    Am I right until here? Do I miss some/ should I change some parameter?
    Last edited by Splinter479; 07-12-2017, 11:26 PM.

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