Where could I find assembly graph?

[marinachen]

Hi OPERA-MS developer,

I would like to ask where I could find the assembly graph. I searched subdirectories in the output folder, but didn't find any gfa or fastg files. It looks like it was generated though according to the checkpoint Long-read mapping and assembly graph generation [2/8]. Thanks for your help!

Best,
Marina

[jsgounot]

Hi Marina,

While OPERA-MS produces an initial assembly graph internally, it is never formatted and saved with the usual assembly format, sorry. If you really want to produce a .gfa file, you would need to merge the initial short-read assembly data with information found within the pairedEdges_above_thresh file. Note that, as it says, this is only step 2 of the OPERA-MS pipeline, and that many more refinements are operated after this initial graph construction to obtain the final assembly.

JS