Re: [Mauve-users] How to deal with 49 bacterial genomes

[Aaron D. <aar...@ut...>]

Hi LiXiang,
The time complexity of the progressiveMauve algorithm scales at least
cubically in the number of genomes being aligned, with length being an
additional approximately n log n factor. In practice that means that
the upper limit for progressiveMauve is usually datasets of around 30-
50 bacterial genomes. It should finish if you continue to wait, but you
may be waiting a very long time. Depending on your analysis goals one
option may be to reduce the set of input genomes.  Do you need pan-
genome alignment or just core genome alignment? If a core genome
alignment is sufficient for your subsequent analysis tasks, you might
have a look at the Harvest tools (parsnp, gingr) by Treangen et al.
Best,
-Aaron
On Sun, 2016-10-16 at 17:04 +0800, LiXiangchen wrote:
> Hi all,
>  
> I used to run progressiveMauve with 49 bacterial genomes, each genome
> is about 13MB. The job has been running for three weeks and is still
> running now. Since I just use all default parameters, I have no idea
> to improve it.
>  
> Can you give me any suggestions? I am very grateful.
>  
>  
> -------------------------------------------------------------------
> -----------
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Mauve-users mailing list
> Mau...@li...
> https://lists.sourceforge.net/lists/listinfo/mauve-users
-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman





UTS CRICOS Provider Code: 00099F
DISCLAIMER: This email message and any accompanying attachments may contain confidential information.
If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or
attachments. If you have received this message in error, please notify the sender immediately and delete
this message. Any views expressed in this message are those of the individual sender, except where the
sender expressly, and with authority, states them to be the views of the University of Technology Sydney.
Before opening any attachments, please check them for viruses and defects.

Think. Green. Do.

Please consider the environment before printing this email.