Afterqc with pypy

[coolmak32]

Hello,
I have a 12 paired end files(50gb~). For each file it takes me 14hrs approx to run with native python. I read that with pypy command it runs 3 times faster. But when i edit my script with pypy command it returs error saying there is no such command. Am i need to download somwthing to use it with pypy command?

[sfchen]

You have to install pypy first. See: http://doc.pypy.org/en/latest/install.html

BTW, I suggest to use fastp, instead of AfterQC. fastp is another tool I developed, providing all AfterQC features, but 10x faster.

fastp is available: https://github.com/OpenGene/fastp

[coolmak32]

I did analyze the first part of my experiment using AfterQc, is it better to use this new tool? I do not want to have variability. Thanks for the above link. Kuldeep Makwana (Ph.D. candidate regulatory biology) SR 271,BGES Cleveland State University. 216-262-9156

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On 4 February 2018 at 19:16, Shifu Chen ***@***.***> wrote: You have to install pypy first. See: http://doc.pypy.org/en/latest/ install.html BTW, I suggest to use fastp, instead of AfterQC. fastp is another tool I developed, providing all AfterQC features, but 10x faster. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#33 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Afd3lo-EgvUpgfzoFcU7ul2igqMT5Ubbks5tRkhtgaJpZM4R4rs7> .

[sfchen]

It provides similar quality, but much higher performance.

But since you have done the first part of analysis using AfterQC, I suggest you to continue use AfterQC for this project.

If you're using Ubuntu, you may be able to install pypy with: sudo apt-get install pypy, or sudo pip install pypy.

If these two commands don't work, you can download and install it manually.