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.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