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Facilities

Computer specifications

Desktop (24 Nos.)
Memory:16GB
Processor: Intel core i7 (3.2GHz)
Hard Disk: 1TB
Graphics card: NVIDIA Geforce GT710 (2GB)
Operating system: Dual operating system (Windows 10 & Ubuntu)
 
High Performance Cluster
Master node
DELL PowerEdge R740xd Rack Server
Processor : 2x Intel Xenon silver 4116 processor (@ 2.10GHz × 48)
: Model 85 Stepping 4
Hard Disk : 4.7TB
RAM : 128 GB
 
 

Compute node


DELL PowerEdge R640 Rack Server
Processor : 2x Intel Xenon silver 4116 processor (@ 2.10GHz × 48)
: Model 85 Stepping 4
Hard Disk : 256GB
RAM : 128 GB
 
Operating system: CentOS Linux 7
Management Embedded / At-the-Server : iDRAC9 (Integrated Dell Remote Access Controller 9)
Firmware version : 4.00.00
 

Software


NGS data analysis (Freeware)
Software

Name of the tool

Function

SRA Toolkit

To convert SRA file into FASTQ format

FastQC

Quality control of NGS raw data

FASTX-Toolkit

NGS data preprocessing

Trimmomatic

Trimming of low quality reads

Trim Galore

Velvet

Genome assemblers

Velvetoptimiser

ABySS

Soap de novo

SPAdes

MaSuRCA

Augustus

Genome annotation

Braker

Prokka

RAST

Prodigal

NCBI-BLAST

Quast

Assembly statistics and quality assessment

Bowtie2

Genome mapping

RepeatModeller

To construct new repeat library

RepeatMasker

Masking repetitive elements in the genome

 
All other major Bioinformatics freeware tools are also used at the Centre.

Translations

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Address

Bioinformatics Centre
College of Agriculture
IT-BT Complex, Kerala Agricultural University Main Campus
Vellanikkara
Thrissur Kerala 680656