Using GFA assembly graphs
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Entering edit mode
15 months ago
dp ▴ 40

Hi

I have been using the assembly graphs output in fastg format by (meta-)SPAdes and megaHIT. They are relatively easy to parse and manipulate in Python - for example, to load the graph structure using networkX and associate sequences, sequence lengths, and depths with the nodes in the graph.

I'm interested in also doing this with the output of other assemblers in GFA format. Is there an easy way to do this in Python? The most important feature for me would be to easily load the graph into networkX and extract the sequences, sequence lengths and coverages from the GFA files.

Thanks!

Assembly GFA • 799 views
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