Question: fastQC for Oxford Nanopore reads
0
gravatar for efratk
8 months ago by
efratk0
efratk0 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 • 1.4k views
ADD COMMENTlink modified 8 months ago • written 8 months ago by efratk0

Thanks a lot for the reply

ADD REPLYlink written 8 months ago by efratk0
3
gravatar for arfesta
8 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 8 months ago by arfesta30
0
gravatar for genomax
8 months ago by
genomax48k
United States
genomax48k wrote:

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

ADD COMMENTlink modified 8 months ago • written 8 months ago by genomax48k
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