Question: How to assemble scaffolds using Galaxy
gravatar for nhpheonix
3.9 years ago by
nhpheonix0 wrote:

I haved downloaded scaffold sequences from the Internet.

Can I use Galaxy to assemble the scaffold sequences? which tools should I choose?

assembly • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by nhpheonix0

What do you mean by assemble scaffold. Scaffolds are already assembled contigs that can't be merged further.

ADD REPLYlink written 3.9 years ago by Bjoern Gruening5.1k

I mean useing the assembled contigs to generate whole genome sequence

ADD REPLYlink written 3.9 years ago by nhpheonix0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Bjoerns comments are correct - but I am wondering of you really mean that you wish to perform some type of analysis with the current assembly you have. Compare to other genomes? Expression/variant analysis (along with NGS reads from specific conditions)? 

A search right here in Galaxy biostars will bring up much prior Q&A on the subject, such as what you are seeing over at the far right -->

You can also examine tutorials and related materials through our wiki/main public Galaxy site. Start here: > Learn, Train, Support, etc. > Pages and if you are familiar with Galaxy, exploring other Shared resources will be helpful

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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