Question: How to make De novo genome assembly?
1
gravatar for mmdiagne
3.1 years ago by
mmdiagne10
United States
mmdiagne10 wrote:

Hi,

I have an account "on Main".I can't find Velvet for De  Novo genome assembly. However i have seen a toturial where it is noticed that we can use this software in Galaxy.

Can you help me to find it or another software which can permit to do De Novo assembly?

Thank you.

 

assembly velvet • 2.0k views
ADD COMMENTlink modified 3.1 years ago by Martin Čech ♦♦ 4.8k • written 3.1 years ago by mmdiagne10

Thank you Martin Čech !

So for being able to use Velvet, i can't be in an account on Main, right?

Do you know if i can actually use another way in Galaxy on Main to perform a De Novo Assembly?

 

ADD REPLYlink written 3.1 years ago by mmdiagne10
2

You can look into assembly section in the https://toolshed.g2.bx.psu.edu/ and you can look for Galaxies with assembly tools are https://wiki.galaxyproject.org/PublicGalaxyServers

 

ADD REPLYlink written 3.1 years ago by Martin Čech ♦♦ 4.8k

I will check these links. I've just seen a a galaxy-based viral genome assembly pipeline clled virAmp. It is on this link:  http://viramp.com/

Do you know it? It seems to be easier for all the different steps of NGS data analysis.

ADD REPLYlink written 3.1 years ago by mmdiagne10
3
gravatar for Martin Čech
3.1 years ago by
Martin Čech ♦♦ 4.8k
United States
Martin Čech ♦♦ 4.8k wrote:

There is a velvet assembler in the Tool Shed (which you can install on your own Galaxy, but it is not on Main) however it might be outdated - last updated on 2011-06-07

This is the link to it: https://toolshed.g2.bx.psu.edu/view/edward-kirton/velvet_toolsuite/4afe13ac23b6
(note that the link above does not install the velvet itself, only the Galaxy part of it, you still need to install velvet on the machine that will run it)

Assemblies are often resource-intense thus not many Galaxies offer their compute power publicly for free.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Martin Čech ♦♦ 4.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 107 users visited in the last hour