Link creation fails on minimal example?

[winni2k]

I have created a gist with the relevant input and log files.

When I run mccortex with kmer size 3 with an input fasta containing two reads of length 4, and I then thread the same reads through the resulting graph, I do not get any links in the links file. Is this a bug, or am I doing something wrong?

[noporpoise]

For a repeat of length L you need a read of length L+2 to pair input and output edges. The shortest repeat in a k=3 graph is 3bp, so you need a read of 5bp covering it to generate links across it. Adding a base at the beginning should generate four links:

>0
GCGTT
>1
CCGTA

[winni2k]

Thanks! That works.

A second question, since we're on this topic: Does mccortex annotate links in through bubbles or does mccortex only annotate through cycles? If not, why not?

[noporpoise]

Links are only added to tangles -- parts of the graph that collapse down then split out again. A simple bubble can be traversed without links if you try walking down all the options one at a time. I'll try to add some better documentation on links - sorry I don't have time right now. The paper on Linked de Bruijn graphs (or my thesis when I upload it) might be the best place to start.

[winni2k]

That's a really succinct description! Thank you so much.

…

On Tue, Oct 16, 2018 at 6:18 PM Isaac Turner ***@***.***> wrote: Links are only added to *tangles* -- parts of the graph that collapse down then split out again. A simple bubble can be traversed without links if you try walking down all the options one at a time. I'll try to add some better documentation on links - sorry I don't have time right now. The paper on Linked de Bruijn graphs <https://academic.oup.com/bioinformatics/article/34/15/2556/4938484> (or my thesis when I upload it) might be the best place to start. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#74 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AASnPrRavAIVRirGtzTNAf5rJnh84O3vks5ulgbVgaJpZM4XNJ4W> .

-- Post-doctoral researcher School of Engineering Sciences in Chemistry, Biotechnology and Health Department of Gene Technology SciLifeLab KTH Royal Institute of Technology Stockholm, Sweden