Question: Computational infrastructure required for RNAseq analysis, genome annotation and assembly of eukaryotic genome
1
gravatar for Leandro de Mattos
5.6 years ago by
Brazil
Leandro de Mattos90 wrote:

Dear, I would like some help! I need to implement a computational infrastructure for my routine analysis of bioinformatics. I would like a suggestion on what would be a minimal or optimal configuration for tasks which can include: genome assembly and annotation, analysis rnaseq (transcriptome), then comparative genomics.

Thanks for attention.

 

EDIT: Post title changed to make it more informative by Ashutosh Pandey.

sequencing • 3.1k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 5.6 years ago by Leandro de Mattos90
2

 

If you are asking about programs and methods, a good starting point is "GATK's best practices":

https://www.broadinstitute.org/gatk/guide/best-practices

 

ADD REPLYlink written 5.5 years ago by Pablo1.9k
2

what is Genome montattion?

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.4k

I apologize, it was written wrong.

ADD REPLYlink written 5.5 years ago by Leandro de Mattos90

So if I understand correctly, you are asking for the hardware settings? Or are you asking for the scripts to perform such tasks?

ADD REPLYlink written 5.5 years ago by Sam2.8k

Hi Sam, my question is about hardware settings. ;D.

ADD REPLYlink written 5.5 years ago by Leandro de Mattos90

Please post comment as comments and not as answers.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by PoGibas4.8k

Thank you Ashutosh Pandey by helpe and information.  Where I need of a structure for routine analysis of RNAseq and genome assembly.   Do you have any sugestion?

 

 

 

 

ADD REPLYlink written 5.4 years ago by Leandro de Mattos90
3
gravatar for Ashutosh Pandey
5.5 years ago by
Philadelphia
Ashutosh Pandey12k wrote:

You should elaborate little more. See below:

1) Will it be just for your use? Or will it be part of a small research lab or some bioinformatics centre with multiple users?

2) Are you considering buying a multi CPU systems or cluster or you are talking about a desktop with good computing power and space (A few of those analyses can be done on desktop machines with descent RAM and memory)

3) Amount of storage capacities will depend on how much new data you are generating and analyzing. We have a md1000 systems that can take 8 X 500 Gb hard disks (4 TB). It is only used for the purpose of analysis and data storage for 6 months once it is out of the machine. We then need to back up those hard disks once every 6 months as our sequencing facility keeps generating new data.      

Some related posts:

A: Best Hardware Solution For Medium-Size Bioinformatics Lab [15-20 Computers]

A: It Architecture For Large, Genomic Data-Backed Application

A: What Are The It Requirements For High Throughput Sequence Analysis

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Ashutosh Pandey12k
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