Bioinformatics & Sequencing Facility

Facility Staff

Konstantinos Krampis

Director

Office: Belfer Research Building, Room 467F
Phone: (212) 396-6930
Email: agbiotec@gmail.com

Lloyd Williams

Director Main Campus

Office: 68th Street Campus, North Building Room 826B
Phone: (212) 650-3872
Email: williams@genectr.hunter.cuny.edu

National Institute on Minority Health and Health Disparities

Facility Description

The Hunter College/CTBR Bioinformatics resources is located on the 4th floor of the Belfer Research Building at 69th Street and York Ave. The facility affords access to researchers and faculty, a high-performance computer cluster with a large range of bioinformatics software and data analysis pipelines. The facility provides cutting-edge bioinformatics technology for translational and basic research on health disparities. We also host a web-accessible bioinformatics platform based on Galaxy, (http://galaxy.hunter.cuny.edu:8080) to support genomic sequencing analysis.
Additionally, the facility offers Illumina Sequencing using the Illumina MiSeq sequencing platform and Nanopore sequencing using Oxford Nanopore MinIon sequencer. Both these instruments are capable of sequencing entire complement of DNA, or genome, of many animal, plant, and microbial species for basic biological and medical research. A detailed description of our services and available equipment is given below

Bioinformatics and Sequencing Facility staff.

Services

RNAseq and variation discovery
small RNAs sequencing
de novo bacterial genomes
RNAseq Analysis
Targeted amplicon sequencing
Computational Capacity
Scalable Storage

Resources and Equipment

Procedure For Submitting Jobs to the Cluster

SLURM, Work Load Manager
Jobs must be submitted to the cluster using Using SLURM, our job management platform. Vitual environments can be loaded using Conda our package manager. Once you activate your environment and you are sure your application is available, you can simply request srun or sbatch. Follow these steps to use SLURM

Get a compute node assigned to you:

[username@ctbr-cluster-hn1 env ]$ salloc
salloc: Granted job allocation 48

Salloc requests resources form the cluster. The number 48 in the example above is the allocation n er provided to you. You can submit jobs directly to your allocation or run a batch script. Submitting a job using the command SRUN that will make use of the resources allocated. For this example we will use Bowtie2.

srun bowtie2 -x Bowtie_2/hg38 -1 RNAseq_sample_dat6a/adrenal_1.fastq -2 RNAseq_sample_data/adrenal_2.fastq -S alignment.sam

srun = Directs the job to the compute node assigned by salloc.
bowtie2 = Main binary inside the virtual environment recently activated.
Bowtie_2/hg38 = This is the reference human genome
RNAseq_sample_data/adrenal_1.fastq = First input strand
RNAseq_sample_data/adrenal_2.fastq = Second input strand
alignment.sam = The output file will be placed in the current directory

A guide on using conda and SLURM can be obtained by clicking here

The Bioinformatics and Sequencing Resources is supported by a Research Centers in Minority Institutions Program grant from the National Institute on Minority Health and Health Disparities (MD007599) of the National Institutes of Health.