Question: fastQC for Oxford Nanopore reads
1
gravatar for efratk
22 months ago by
efratk10
efratk10 wrote:

Hi,

I want to use fastQC for quality control checks on nanopore sequencing reads. When I ran fastQC it ran a long time without finishing or given an error. I stopped the job after several hours and got an error: "java.lang.OutOfMemoryError: Java heap space" What is the reason for it? Is fastQC good for nanopre reads? (I read that fastQC added support for processing files of Oxford Nanopore reads), Which other tools are recommended for quality control checks on nanopore sequencing reads?

Thanks

sequencing assembly • 4.5k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by efratk10

Thanks a lot for the reply

ADD REPLYlink written 22 months ago by efratk10
3
gravatar for arfesta
22 months ago by
arfesta30
arfesta30 wrote:

Here are a few tools I've used..I think the question comes down to what exactly do you mean by QC (what stats are you trying to find out):

minion_qc

IONiser

Nanoplot..as seen here on biostars

ADD COMMENTlink written 22 months ago by arfesta30
0
gravatar for genomax
22 months ago by
genomax70k
United States
genomax70k wrote:

See posts #358-359 in this thread for a possible solution.

ADD COMMENTlink modified 22 months ago • written 22 months ago by genomax70k
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