AllPaths workflow question

[crusoe]

Jumping (>>1Kb inserts) reads are required to use AllPaths-LG. I'd look at the many other excellent assemblers without that requirement (though jumping reads are very useful for all assemblers)

[csmatyi]

Hello,

<REF>/<DATA>/frag_reads_orig.fastb
<REF>/<DATA>/frag_reads_orig.qualb
<REF>/<DATA>/frag_reads_orig.pairs
<REF>/<DATA>/jump_reads_orig.fastb
<REF>/<DATA>/jump_reads_orig.qualb
<REF>/<DATA>/jump_reads_orig.pairs
These files are needed by the /arch/AllPathsLG/bin/PrepareAllPathsInputs.pl script used by allpaths. How do I make them? I only have short reads, no jump sequences.

[crusoe]

I would second the posting of your question to the user forum.

Use a computer that has access to the filesystem where your run is (could be the same host or another one). Run your pipeline again with the same arguments and add DRY_RUN=True to see what else needs doing.

Ignore any errors about the current module not being finished (which is true).

You can also cause it to output an HTML page with the pipeline as you've configured it with the parameter VIEW_PIPELINE_AND_QUIT=True.

Assuming you're not using the optional long jumps or long reads then you have about 14 modules to go.

Good luck!

[crusoe]

This a great question for the Allpaths-LG user forum: https://groups.google.com/a/broadins...ths-user-forum

[dray]

Hi all. I'm assembling a eukaryotic genome with AllPaths. It's been moving along nicely for nearly three weeks and I'm hoping that the end is near. However, I can't find information on the processes that still need to be accomplished. As of this morning, the package started with RemoveHighCNAligns. Does anyone know of a list of the processes involved in AllPaths so I can get an idea of where I am in the entire assembly process?

Thanks.

David