Indian Council of Agricultural Research
(Agricultural Knowledge Management Information System)


ICAR-Central Research Institute for Jute & Allied Fibres, Barrackpore, Kolkata-700121 West Bengal (https://crijaf.icar.gov.in)
Click Here to See Management Committee
Instrument Details
Instrument/Facility Name: Genome station for Bioinformatic analysis
Make                                   : DELL
Model                                  : Precision Tower 7810 Server (optimized by Bionivid Bionivid Technology Pvt. Ltd., Bengaluru, India)
Specification   :Memory – 64 GB (4 x 16 GB); DDR4; Processor – Intel ® Xeon ® 2.40 GHz x 16 cores; Disk space – 3.9 TB with additional external hard drives; Operating system – Ubuntu 14.04 LTS 64-bit; Standard Softwares for NGS analysis, such as FASTQC, Trimmomatic, Trinity, RSEM, TopHat-Cufflinks, Interproscan, basic Blast2GO, standalone NCBI Blast v. 2.4.0, Microsatellite Identification software (MISA), Perl, Bowtie2, AUGUSTUS etc.

Click to ViewGenome Stations/ Workstation is a performance optimized large-scale genomics data analysis devise. This power-packed multi-processor server is sufficient to handle moderate data load of transcriptome sequence and genome sequences of prokaryotes and plants with smaller genome sizes. The instrument is backed-up with all required softwares for quality checking and analyzing of the raw NGS reads to assemble contigs and annotation of the assembled contigs. A complete pipeline of softwares are installed for NGS analysis, molecular marker development and NCBI-Blast analysis. With the power of command line scripts, it is possible to easily resolve the difficulties of large-scale data handling, analysis and interpretation of results to address any biological questions at the molecular level.

  Working Principles
Click to ViewAll the analysis in genome station runs by the machine learning process using standard or customized linux and perl scripts. All the softwares used in the analytical process are available at the public domain under the GNU General Public License

  Applications
  User Instructions
Any Next-generation sequence analysis, RNA-seq/Transcriptome assembly (both de novo and genome-guided), Small-scale genome sequence assembly (Prokaryotes), Meta-genomics sequence assembly and annotations, Molecular markers (SSR and SNP) discovery etc.All users should possess a basic knowledge of linux/unix commands and technical know-how of the softwares to be run for the desired purpose. Alternatively, may take the help of the expert(s) available at the Centre. Users must comply with the limitations of the machine to handle extremely large data size, which may lead to system/memory crash. All users must sign the logbook for using the machine.

  Contact Us
Contact No. 033-25356121(Ext No.209)
Email Id crijaf-wb@nic.in / director.crijaf@icar.gov.in

  Genome station for Bioinformatic analysis Charges
Procedure Name
Industry
University
National LAB/R&D
Remark
Genomics data analysis

Additional Rs 100/-towards postal charges if result are to be posted
The Demand Draft should be in favour of "ICAR UNIT CRIJAF, BARRACKPORE"
Letter, DD & Samples send to "The Director, ICAR-CRIJAF, Barrackpore, North 24 Parganas, West Bengal 700120 "