cleaning NGS Data: tool?

Question

[midox]

Hello,

I want to do a cleaning of my data (short and long reads reads) to minimize the error rate. Do you suggest me good cleaning tools?

Thank you

[Pas]

But when you do a NGS experiment, in theory all the reads should have the same length.

Which kind of experiment you are doing?

[Brice Sarver]

Not necessarily if you are combining reads from different platforms or earlier chemistries. Data is still data. You might want to consider asking for clarification in a comment as opposed to an answer.

[Pas]

You are right,

Since he wrote "my data", It was not clear to me that midox's data were from different platforms or that have been generated with different chemistry. In this case one must be very cautious in integrating these data because the level of noise can be very high.

[midox]

Thank you for your response.

Yes, I have data (short and long reads) from different platforms and this data are very noisy and I want to clean them for my experiments.

Thank you for your response.

Answer 1

[5heikki]

I like TrimGalore, which is basically a wrapper for cutadapt and FastQC.

[midox]

I did some research I found QCtoolkit. What do you think of this tool? Thanks for your answer