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 Read more…
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 Read more…
Sometimes after demultiplexing there exists a high number of undetermined reads, i.e. reads which were not assigned to any library based on the barcodes provided. This is most often the result of incorrect metadata or barcode contamination. Determining what barcodes Read more…
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 Read more…
Update 7/21/2021: reform has officially been published as an NFT. Read about this experiment in scientific publishing here. Access the reform publication (PDF) here. Update 11/20/2019: reform is now available as a web app https://reform.bio.nyu.edu/ reform is a python-based command Read more…
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. Read more…
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 Read more…
Save time and resources with the local CGSB repository of commonly used genomic data sets. Data is obtained from Ensembl and NCBI. New versions/releases will be added periodically or upon request. Previous versions/releases will be preserved. All files are readable Read more…
Connect to Prince using a remote desktop to analyze your data in RStudio, visualize in IGV, and interact with other GUI applications on the HPC.
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 Read more…