merged.fasta the same as hybrid_assembly.fasta about quickmerge HOT 11 CLOSED

from quickmerge.

Sure. First I sourced the .quickmergerc, then:

for the wrapper:
merge_wrapper.py hybrid_assembly.fasta self_assembly.fasta

which finished with no errors.

Then with individual steps as:

nucmer -l 100 -prefix out self_assembly.fasta hybrid_assembly.fasta
delta-filter -i 95 -r -q out.delta > out.rq.delta
quickmerge -d out.rq.delta -q hybrid_assembly.fasta -r self_assembly.fasta -hco 5.0 -c 1.5 -l 400000 -ml 5000

which also didn't show any errors. Both resulted in the same output content described above.

from quickmerge.

from quickmerge.

Yes. Would it be useful to upload this file?

from quickmerge.

from quickmerge.

You can download the file using the following link:
https://www.dropbox.com/s/5qlld3k2m0n4da4/out.rq.delta.gz

And the 400kb n50 is from the self-assembly file.

from quickmerge.

from quickmerge.

The reads almost certainly derive from the same species. One point that could be important is that the self_assembly.fasta is almost 50% larger than the expected genome size, which is probably the result of redundancy in the assembly. Do you think this redundancy could result in the type of whole genome alignment results being observed here?

from quickmerge.

If there is high homology between the two assemblies then it should show HCO >5. Will you be able to share the fasta files so that we can investigate this a little more. We will use your files only to understand the problem and will not share it with anyone else. Let us know.

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Do you have a preferred email address where the files could be sent to?

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from quickmerge.