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Old 01-27-2016, 06:50 PM   #1
jmartin
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Location: St. Louis

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Posts: 71
Default Problems running nanocorr error correction w/ illumina reads and pacbio data

I have an assembly of a nematode genome (~410Mb in size) that was originally created from 454 data, and then later improved with PacBio data using PBJelly. I would now like to try and error correct this data using 30x coverage of Illumina reads and the NANOCORR software, but I'm having some trouble understanding how to run it.

Looking at the README, I see that I am supposed to run a partition script on what would be the nanopre_reads, but in my case I don't have that. The reads I want to use to improve my assembly are Illumina reads. So should I be partitioning the Illumina reads instead?

Then, the actual nanocorr command line is basically this:

nanocorr.py query.fa reference.fa

and the software README says:
++++
The query file will be "blasted" against each previously partitioned read.
This query file can be anything useful for correction.
Illumina data is what is used right now.
++++

So this is what confuses me. I know the typical usage of nanocorr would be to have nanopore reads, illumina reads, and a reference. In my case I have only an assembly that I want to error correct, and illumina reads. Technically I also have PacBio data, but I have already improved my assembly using that data via PBJelly. I just want to error correct this assembly using the illumina data. Can nanocorr help me in this case? A co-worker who recently left said he had been using nanocorr to do this kind of thing, but when I look at it, it seems like this is not the typical usage. And the documentation he left behind is not very complete.

If anybody here has experience with nanocorr I'd really appreciate some advice.

Thanks,
John
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Old 01-28-2016, 12:03 PM   #2
rhall
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Default

Try https://github.com/broadinstitute/pilon which was designed for this task.
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