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lbcb-sci / raven

De novo genome assembler for long uncorrected reads
MIT License
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How to draw layout graph as in the raven publication #82

Open yipukangda opened 6 months ago

yipukangda commented 6 months ago

Hi,

I assembly a plasmid sequence data with raven but get no fasta output, but there are three seq records in gfa file(I run flye and canu with same sequence file and all output an assembled sequence), I think if I can draw the layout graph of reads overlap, maybe it can offer me some clues about where the problem is. But I do not find the tool and code for drawing in this repo, so I ask for your help here.

Thanks

FilipTomas commented 6 months ago

Hi, If I understand correctly, you do get an output, but in gfa format and not in fasta? In this case, you may use Bandage (https://github.com/rrwick/Bandage) to draw the assembled contigs. If you want to get the fasta format out of a gfa file you can use: awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

Kind regards

yipukangda commented 6 months ago

@FilipTomas Hi, I mean the fig 1 in the raven publication: https://www.nature.com/articles/s43588-021-00073-4, it seems draw from reads overlap and with some post processing to mark reliable paths.

Thanks

FilipTomas commented 6 months ago

Hi,

The graphs were likely plotted using the plotter.py script located in the misc folder. The script requires a graph in JSON format. However, I've tested the JSON printing function in Raven, and it appears to not be functioning correctly at the moment. I'll investigate and work on fixing that.

Alternatively, you might consider using Graphia or Cytoscape as other options.

Kind regards

yipukangda commented 6 months ago

@FilipTomas Thanks, if I want to draw the layout graph with tools your recommend, I need to wait until you fix the JSON output to get overlap information, right?

FilipTomas commented 5 months ago

Hi, sry for the late reply :) You can use the gfa output, using the --graphical-fragment-assembly option. Another tool you can use is gfaviz.

yipukangda commented 5 months ago

Hi, --graphical-fragment-assembly just output a consensus path, but what I want is the raw overlap graph from raw reads for check what is the wrong maybe within the layout step.