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Performance

Speeding Up UMI-tools with Cython: A 4.6x Performance Win

Speeding Up UMI-tools with Cython: A 4.6x Performance Win

Overview You know that feeling when you're running a bioinformatics pipeline and you watch the progress bar crawl along at a glacial pace? You grab a coffee, check your email, maybe start a second analysis on another dataset... and 90 seconds later your first job is still processing

Bioinformatics Pipeline Engineering: Do This Not That: Split Tasks

Bioinformatics Pipeline Engineering: Do This Not That: Split Tasks

Overview In the last installment of this series, we talked about how to handle large files without bringing down the wrath of your local sys admin. Today we're tackling how to think about breaking up tasks. You've probably written it. I've definitely written it.

Bioinformatics Pipeline Engineering: Do This Not That: Large Files

Bioinformatics Pipeline Engineering: Do This Not That: Large Files

Overview If you've worked with bioinformatics data, you've likely encountered the dreaded experience: your Python script chugging along, consuming memory at an alarming rate, and then—crash. Out of memory. Your computer becomes unresponsive, and you're left frustrated wondering why your beautiful analysis script