Post Genome Assembly

Question

[div]

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?

[orange]

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)

[div]

@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....:)

[orange]

When I click "ADD COMMENT" or "ADD REPLY" (color of the button is gray), but it did not work. Someone tell me why?

[div]

It works....:) Once you log out and then again log in and check...:)

Answer 1

[HG]

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

http://contiguator.sourceforge.net/

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

[div]

@ HG

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

Answer 2

[kcamnairb]

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.

[orange]

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

[mgalactus]

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