feature request: command line arguments & support of separate UMI file

BiodataAnalysisGroup / UMIc

A framework implementing a method for UMI deduplication and reads correction.

MIT License

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feature request: command line arguments & support of separate UMI file #1

Open koriege opened 2 years ago

koriege commented 2 years ago

Hi,

I really appreciate your work. But to use your tool in a more comfortable way and being able to deal with many input files, it would be nice to have command line options available. Further, typically I am dealing with UMIs stored in a separate fastq.gz file and thus need to extract, paste and re-compress all my files, which is very time consuming. Btw. do you think it would be possible to support multi threading?

npechl commented 1 year ago

Hi @koriege,

Apologies for the late answer.

UMIc is running as a collection of R scripts. We are planning on making it a stand-alone R package, in order to be more robust and user-friendly.

We also thank you for your suggestions on improvements to the tool. We will work on adding them in a future version.

Regards, Nikos