Analyze your Data Faster with NASQAR: Nucleic Acid SeQuence Analysis Resource

Analyze your Data Faster with NASQAR: Nucleic Acid SeQuence Analysis Resource

The bioinformatics team at the NYU Center for Genomics and Systems Biology in Abu Dhabi and New York have recently developed NASQAR (Nucleic Acid SeQuence Analysis Resource), a web-based platform providing an intuitive interface to popular R-based bioinformatics data analysis and visualization tools including Seurat, DESeq2, Shaman, clusterProfiler, and more. These tools, although powerful, typically… [read more]

GPU-Accelerated MinION Basecalling On the HPC

GPU-Accelerated MinION Basecalling On the HPC

I recently helped the Rockman lab basecall their MinION sequencing data on the 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 desktop. Since more people are beginning… [read more]

Beginners Guide: What is OpenStack?

Beginners Guide: What is OpenStack?

OpenStack, a project originally started by NASA and Rackspace, is an open source cloud computing platform that enables users to access and control pools of compute, storage, and networking resources. TechCrunch calls it “one of the most important and complex open-source projects you’ve never heard of”. Like competitor Amazon Web Services (AWS) and other cloud… [read more]

reform: Modify Reference Sequence and Annotation Files Quickly and Easily

reform: Modify Reference Sequence and Annotation Files Quickly and Easily

reform is a python-based command line tool that allows for fast, easy and robust editing of reference genome sequence and annotation files. With the increase in use of genome editing tools such as CRISPR/Cas9, and the use of reference genome based analyses, the ability to edit existing reference genome sequences and annotations to include novel… [read more]

Next-Generation Sequencing Analysis Resources

Next-Generation Sequencing Analysis Resources

The NYU Center For Genomics and Systems Biology in New York and Abu Dhabi have developed a new website with resources for mastering NGS analysis: https://learn.gencore.bio.nyu.edu/ Modules are designed to provide hands on experience with analyzing next generation sequencing data. Standard pipelines are presented that provide the user with and step-by-step guide to using state… [read more]

Salmon & kallisto: Rapid Transcript Quantification for RNA-Seq Data

Salmon & kallisto: Rapid Transcript Quantification for RNA-Seq Data

Salmon and kallisto might sound like a tasty entree from a hip Tribeca restaurant, but the duo are in fact a pair of next-generation applications for rapid transcript quantification. They represent a new approach to transcript quantification using NGS that has a number of advantages over existing alignment-based methods. I’ve tried them both out and… [read more]

Node to Joy: Maximize Your Performance on the HPC

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… [read more]

The Genomics Core Facility (Gencore) is a state of the art genomics facility enabling high throughput genome sequencing, proteomics and quantitative analyses.

Gencore is located in the Center for Genomics and Systems Biology in the Biology Department at NYU-NY and the Center for Genomics and Systems Biology in NYU-AD.

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