Error: Segmentation fault (core dumped)

[opengene]

Error: Segmentation fault (core dumped)

[sfchen]

I will check with the sliding window cutting by quality.

Thanks

[sfchen]

I just update the code to fix this issue, please try the latest version and update here.

Big thanks for your contribution.

[haiwufan]

Thanks sfchen，
I will test the lastest version, thanks again.

[haiwufan]

Hi sfchen,
Today, I compared three software (fastp, cutadapt, trimmomatic) , and found fastp very fast but adapter cannot be remove clean.
I upload my result and hopefully you found this useful!

compare_software.xlsx

[sfchen]

Thanks for the result, from the data, I can see:

• for short adapters (7bp), Trimmomatic removes the most adapter, then fastp removes less, and Cutadapt removes the least.
• for longer adapters (>7bp), fastp removes much more than Trimmomatic and Cutadapt.
• in total, fastp removes the most adapters.

Am I right?

[sfchen]

Can you try to grep the adapter sequence in those files?

Can you open another issue so we can track it with a new title, since the segmentation fault issue is already fixed.

Can you upload the first 10000 lines of the FASTQ files? So I can test it?

[sfchen]

Closing this issue.