merging self pacbio assembly with illumina-based one about quickmerge HOT 4 CLOSED

Hi Pedro,

here are the answers for your queries -

a) Your interpretations of reference and query sequences in the wrapper are correct. The reference sequence names in the merged assembly are those that resulted from merging. The name of a merged sequence comes from the sequence name of the anchor reference sequence. So the lengths of such sequences would not match the length of the sequences with the same name in the reference assembly.
e.g. if ref1 -q5-ref3-q7 is the chain that will be merged, where ref3 is the anchor sequence, the merged sequence will be called ref3 in the merged assembly.
the query assemblies that do not participate in merging remain unchanged.

b) It probably is ok to provide scaffolds but we have not tested this.

c) I have not tested it using illumina assembly but a colleague of mine has, and he found improvements in his assembly after using quickmerge. Have you tried DBG2OLC and create a hybrid assembly with your PacBio and illumina reads ?
Please let me know if I missed anything or if you have any other question.
Mahul

from quickmerge.

Hello Mahul,

Back from vacations, thanks for the answer, that covers all my doubts.

About c) - We considered running DB2OLC, but given the priority for other tasks in our server and the comments by other users regarding the running time, we decided to skip it.

Best,
Pedro

from quickmerge.

Hi @mahulchak ,

Thanks for the amazing tool you developed.

Based on your comments

The reference sequence names in the merged assembly are those that resulted from merging. The name of a merged sequence comes from the sequence name of the anchor reference sequence. So the lengths of such sequences would not match the length of the sequences with the same name in the reference assembly.

In my case, I found some of (not all) quickmerge resulting sequences are with reference sequence name but are with exactly same length with that reference sequence. Could I interpret that as there are some of my query sequences are completely contained by my reference sequences?

My quickmerge commit is 3be7287, which I think the most updated version. FYI.

Thank you very much!

from quickmerge.

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