Question: Combining nanopore libraries
0
gravatar for mrmrwinter
2 days ago by
mrmrwinter20
University of Hull
mrmrwinter20 wrote:

Hi

I have two PromethION libraries, one standard, and the other with ultralong read chemistry.

To create a draft assembly i pooled the fastqs of both libraries and assembled from the result.

Now i am coming to nanopolishing the assembly and it requires the fast5 signal files of reads used in the assembly, which are still seperate and unpooled.

Can i just pool the fast5s? This seems difficult due to nanopolish needing the sequencing_summary.txt file, of which there is a separate one for each library.

Should i not have pooled the fastqs for assembly, and instead just use the ultralong readas to scaffold?

ADD COMMENTlink modified 6 hours ago by colindaven2.5k • written 2 days ago by mrmrwinter20
  • multi_to_single_fast5 script on this page.
  • poretools combine (LINK) - this may not exactly be what you need.
ADD REPLYlink modified 2 days ago • written 2 days ago by genomax92k
1
gravatar for colindaven
6 hours ago by
colindaven2.5k
Hannover Medical School
colindaven2.5k wrote:

I think you can just cat the sequencing_summary.txt together if you want to pack the libraries together (not sure if they even have a header).

I had this exact issue with nanopolish. Also, I think you can add multiple separate libraries if my memory serves ... (but it was > 1 year ago).

To be specific, you can use the -d option many times:

nanopolish index -d fast5_1 -d fast5_2 x.fastq
ADD COMMENTlink written 6 hours ago by colindaven2.5k

Awesome, thanks. This is exactly what i needed

ADD REPLYlink written 10 minutes ago by mrmrwinter20
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