Question: Metagenomic Analysis and Megablast
gravatar for Ali
4.3 years ago by
United States
Ali20 wrote:


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,



Tool name: Megablast
Tool version: 1.2.0
Tool ID:
ToolShed URL:


megablast • 1.2k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by Ali20
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The best strategy when using the public Main instance ( 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.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
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