Question: Comparing the Single and Paired End Assemblies
gravatar for sabina.zoledowska
2.8 years ago by
sabina.zoledowska0 wrote:

Hello there!


Im using this touorial to analyze and assembly mate pair NGS reads for my illumina reads :

Right now im almost at the last step: Comparing the Single and Paired End Assemblies. And there is a slight problem, because in the toutorial i should use: 

"From NGS: QC and manipulation, run Count Fasta on each of the contig sets

  • Start with default bin size (100) for each, but then maybe increase for PE assembly?
  • Note the differences in number of sequences and in N50
  • Which might be the “better” assembly?"

And after these procedure i should run lastz on my data (i've sucessfuly uploaded fasta data for my reference genome). 

The problem is that in galaxy there is NO option "count fasta" :(, or at least on:

Could somebody tell me where i can find these tool?

Also maybe some of you have a better workflow to analyze mate pair read of Illumina to assembly the genome on basics of closed reference genome? 

thank you very much for help. im very lost


software error • 1.0k views
ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by sabina.zoledowska0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Contacting the UC Davis training group is probably the best way to address most of your questions about their training protocol:

I can let you know that different public Galaxy servers host different suites of tools. You can always run your own local or cloud Galaxy. That way the installed tools are your choice. AWS offers grants for educational purposes to help with costs of using the cloud infrastructure (Galaxy itself is always free).

Thanks, Jen, Galaxy team


ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k
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