Question: fastQC for Oxford Nanopore reads
1
gravatar for efratk
2.2 years 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 • 5.3k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by efratk10

Thanks a lot for the reply

ADD REPLYlink written 2.2 years ago by efratk10
3
gravatar for arfesta
2.2 years 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 2.2 years ago by arfesta30
0
gravatar for genomax
2.2 years ago by
genomax74k
United States
genomax74k wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax74k
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