multithreading

[KField-Bucknell]

Is there a way to limit the number of threads that the program uses? It looks like it is running one thread per fastq file, but I would like it to only run a limited number of threads on our HPC node. I suppose that I could run afterqc on only a limited number of fastq files at a time, but I thought that there might be a more elegant solution. Thanks, Ken

[sfchen]

Thanks @KField-Bucknell Will implement this feature.

[sfchen]

Before this thread limiting feature is implemented, you can use AfterQC for a single file/pair.

For example

python after.py   -1 read1.fq.gz  -2 read2.fq.gz

Please find more details in the document

[sfchen]

I will implement this feature and make a release in this week.

[serbulent]

Hello,

I couldn't see the multihread option in any release nor in documentation after this comment. Is it implented or still in the waiting list ?

Thanks,

Serbulent

[sfchen]

@serbulent I am sorry that I haven't implemented this for AfterQC.

However, I've implemented another tool fastp, which provides most features of AfterQC, and is much much faster than AfterQC (10X faster), since it's developed in C++ with multithreading.

You can try fastp first: https://github.com/OpenGene/fastp