Genome alignment

Jayakumar S · 12-02-2016, 08:53 PM

Hi,
Planning to align the scaffolds with the reference genome already available. The size of the reference genome is about 3 gb.
Kindly suggest any suitable methods/softwares for the same.
Presently I am trying with MUMmer 2.

regards,
Jayakumar S

fahmida · 12-03-2016, 07:36 AM

You may try Quast:
http://bioinf.spbau.ru/en/quast

Jayakumar S · 12-04-2016, 04:30 PM

Thank you for the suggestion.
Will try for that and let you know.

Jayakumar S

GenoMax · 12-04-2016, 04:45 PM

If the scaffolds are long (e.g. 10's of kb) then you may want to use LASTZ.

Ali May · 12-04-2016, 08:30 PM

From my experience what tool to use depends on why you want to do the assembly.

The last time I wanted to order scaffolds I used Mauve, but this was for a 3 MB genome with less than 15 scaffolds.

You might also want to have a look at
https://omictools.com/whole-genome-alignment-category
and
https://www.biostars.org/p/3511/

I personally make good use of the dev version of BRIG when I want to quickly see how my scaffolds map to a reference microbial genome.

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12-02-2016, 08:53 PM	#1
Jayakumar S Member Location: India Join Date: Sep 2013 Posts: 34	Genome alignment Hi, Planning to align the scaffolds with the reference genome already available. The size of the reference genome is about 3 gb. Kindly suggest any suitable methods/softwares for the same. Presently I am trying with MUMmer 2. regards, Jayakumar S

12-03-2016, 07:36 AM	#2
fahmida Member Location: Australia Join Date: Aug 2010 Posts: 54	You may try Quast: http://bioinf.spbau.ru/en/quast

12-04-2016, 04:30 PM	#3
Jayakumar S Member Location: India Join Date: Sep 2013 Posts: 34	Thank you for the suggestion. Will try for that and let you know. Jayakumar S

12-04-2016, 04:45 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	If the scaffolds are long (e.g. 10's of kb) then you may want to use LASTZ.

12-04-2016, 08:30 PM	#5
Ali May Member Location: Netherlands Join Date: Aug 2016 Posts: 12	From my experience what tool to use depends on why you want to do the assembly. The last time I wanted to order scaffolds I used Mauve, but this was for a 3 MB genome with less than 15 scaffolds. You might also want to have a look at https://omictools.com/whole-genome-alignment-category and https://www.biostars.org/p/3511/ I personally make good use of the dev version of BRIG when I want to quickly see how my scaffolds map to a reference microbial genome.