Question: Post Genome Assembly
0
gravatar for div
5.3 years ago by
div60
Banglore
div60 wrote:

I am having single end reads from Ion Torrent. I assembled the reads by de novo and obtained alot of contigs. May I know what is the recommended software to arrange the contigs into a scaffold?

ADD COMMENTlink modified 5.2 years ago by orange30 • written 5.3 years ago by div60
2
gravatar for HG
5.3 years ago by
HG1.1k
Germany
HG1.1k wrote:

You can have a try with "Contiguator" or "CAR"

http://contiguator.sourceforge.net/

http://www.biomedcentral.com/1471-2105/15/381

 

 

ADD COMMENTlink written 5.3 years ago by HG1.1k

@ HG

Thank you for the suggestion i will definitely use both and check...:)

ADD REPLYlink written 5.3 years ago by div60
2
gravatar for kcamnairb
5.2 years ago by
kcamnairb40
United States
kcamnairb40 wrote:

There doesn't seem to be a publication available for this software yet, but I've found Medusa to be very useful:

https://github.com/combogenomics/medusa

It seems like many of the other scaffolding tools require paired-end reads or are designed for prokaryote genomes.

ADD COMMENTlink written 5.2 years ago by kcamnairb40
1

Hi, the medusa paper came out a few weeks ago, if you are still interested in it

ADD REPLYlink written 5.1 years ago by mgalactus730
1
gravatar for orange
5.2 years ago by
orange30
Korea, Republic Of
orange30 wrote:

Contiguator or Medusa seem to be based reference genome,so it is not denovo ...

ADD COMMENTlink written 5.2 years ago by orange30
0
gravatar for orange
5.2 years ago by
orange30
Korea, Republic Of
orange30 wrote:

you have what type reads to scaffold? Some people have do evaluation of assembly
scaffolding tools( https://rmcsoftwareinc.files.wordpress.com/2015/02/hunt_scaffolding_tools.pdf

ADD COMMENTlink written 5.2 years ago by orange30

@ Orange 

I have single end reads from Ion torrent and my aim is to remove gaps from the scaffolds and also to check whether number of contigs are decreasing or not but for this i can use reference only to check whether the alignment is correct or not other than this i cant use reference for filling gaps and all.

Any suggestion will be a great help

Thank you....:)

ADD REPLYlink written 5.2 years ago by div60
0
gravatar for orange
5.2 years ago by
orange30
Korea, Republic Of
orange30 wrote:

when I click "ADD COMMENT " or "ADD REPLY"(color of the button is gray),but it didnot work ..someome tell me why ?

ADD COMMENTlink written 5.2 years ago by orange30

it works....:) once you log out and then again log in and check...:)


 

ADD REPLYlink written 5.2 years ago by div60
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