SEQanswers Reconstructing a de Bruijn Graph from Velvet's LastGraph
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 Similar Threads Thread Thread Starter Forum Replies Last Post holmrenser Bioinformatics 0 07-17-2013 08:35 AM samanta General 2 03-27-2013 08:34 AM samanta Bioinformatics 0 03-26-2013 07:52 PM Wizard50 Bioinformatics 4 09-13-2012 09:13 PM

 07-12-2017, 06:11 AM #1 Splinter479 Junior Member   Location: Berlin, Germany Join Date: Aug 2012 Posts: 6 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; 07-13-2017 at 12:26 AM.

 Tags de bruijn graph, lastgraph, velvet

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