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Question: Metagenomic Analysis and Megablast
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gravatar for Ali
4.3 years ago by
Ali • 20
United States
Ali • 20 wrote:

Hi,

I am using the windshield splatter workflow to analyse my amplicons, However Galaxy Megablast can not handle Miseq PE reads due to the large nb of reads compared to 454. I appreciate if someone would suggest to me how it can be dealt with.

1- Doing local Megablast would still take huge amount of time for each sample

2 - If Assembling PE reads into contigs and blasting this reference would solve the problem but how to go from there using Galaxy?

Thanks for your help,

Ali

 

Tool name: Megablast
Tool version: 1.2.0
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/megablast_wrapper

 
megablast • 1.2k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by Ali • 20
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The best strategy when using the public Main instance (http://usegalaxy.org) is often to break jobs up into smaller chunks. This is a good idea for many large datasets, regardless of technology. The other option is to move to a cloud instance with more resources.
http://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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