fastQC for Oxford Nanopore reads

Question

[efratk]

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

[efratk]

Thanks a lot for the reply

Answer 1

[arfesta]

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

Answer 2

[GenoMax]

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