Blog

Node to Joy: Maximize Your Performance on the HPC

In this post we’ll discuss maximizing your performance on the HPC. This entry is aimed towards experienced HPC users; for new users, please see Getting Started on the HPC. Recent advances in sequencing technology have made High Performance Computing (HPC) more critical than ever in data-driven biological research. NYU’s HPC resources are available to all NYU faculty, staff, and faculty-sponsored students. Familiarizing yourself with NYU’s HPC resources, and optimizing your use of this technology will Read more

By Mohammed Khalfan, ago
SNPs in IGV

Variant Calling Pipeline: FastQ to Annotated SNPs in Hours

Update: This pipeline is now deprecated. See the updated version of the variant calling pipeline using GATK4. Identifying genomic variants, such as single nucleotide polymorphisms (SNPs) and DNA insertions and deletions (indels), can play an important role in scientific discovery. To this end, a pipeline has been developed to allow researchers at the CGSB to rapidly identify and annotate variants. The pipeline employs the Genome Analysis Toolkit (GATK) to perform variant calling and is based Read more

By Mohammed Khalfan, ago

Start the New Year Off Right: How to Choose the Right Sequencer

A new year means new sequencing projects, but how do you know which sequencer is right for your project? There are many factors that go into choosing which sequencing platform and machine will fit your specific project. Factors that must be considered are time, cost, and depth. Making the wrong decision can lead to more time and more money. Three main things to consider when choosing what run configuration is needed and subsequently which instrument will be used are: Read Length Read more

By Tara Rock, ago