slurm – Genomics Core at NYU CGSB

Bioinformatics

GPU-Accelerated MinION Basecalling On the HPC

I recently helped the Rockman lab basecall their MinION sequencing data on the Prince HPC, leveraging the power of the GPUs available there. This allowed us to bring the total time required for basecalling down to around five hours, from the two weeks(!) it was going to take on the Read more…

By Mohammed Khalfan, 6 years2019-05-30 ago

Bioinformatics

Building an Analysis Pipeline for HPC using Python

In this post we will build a pipeline for the HPC using Python 3. We will begin by building the foundation for a pipeline in Python in part 1, and then use that to build a simple NGS analysis pipeline in part 2. At NYU, we submit jobs to the Read more…

By Mohammed Khalfan, 7 years2018-04-05 ago