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 are present in the undetermined reads can be useful in 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 open-source projects you’ve never heard of”. Like competitor Amazon Web 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 line tool that allows for fast, easy and robust editing 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. Standard pipelines are presented that provide the user with and 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 in part 2. At NYU, we submit jobs to the 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 from within the shared genome resource. There is no need 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 has a number of advantages over existing alignment-based methods. I’ve Read more…
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 Read more…
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 Read more…