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.