Question: Alternatives To Newbler To Assemble Ion Torrent Reads?
3
gravatar for 14134125465346445
6.0 years ago by
United Kingdom
141341254653464453.4k wrote:

What are good alternatives to Newbler to assemble Ion Torrent reads?

assembly ion-torrent • 2.9k views
ADD COMMENTlink modified 5.0 years ago by JC7.8k • written 6.0 years ago by 141341254653464453.4k
5
gravatar for Arpitha Hebbar
6.0 years ago by
India
Arpitha Hebbar200 wrote:

hey, u can use MIRA (Mimicking Intelligent Read Assembly) software. works well with 454, solexa, ion-torrent, pacific bios. its a freely available standalone unix based software. u can download it from this link. http://sourceforge.net/projects/mira-assembler/files/. working procedure also very elaborately explained in the manual.

ADD COMMENTlink written 6.0 years ago by Arpitha Hebbar200
0
gravatar for JC
5.0 years ago by
JC7.8k
Mexico
JC7.8k wrote:

I have been using SPAdes http://bioinf.spbau.ru/spades without problems.

ADD COMMENTlink written 5.0 years ago by JC7.8k

I have been trying to compare SPades with mira for Ion Torrent, but mira is doing a much better job, would you mind saying what command line parameters you are using for SPades?

ADD REPLYlink written 4.9 years ago by Adam Witney10
1

Some bug was introduced into SPAdes post 3.1.0 release that deteriorates performance on Ion Torrent reads. The developers are aware of it although it was never mentioned in e.g. release notes. So I guess, best options right now are SPAdes 3.1.0 and latest MIRA. Newbler might be good, but it's not open source. Somebody should really write a spanking new OLC-based microbial genome assembler for longish reads.
 

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by 5heikki8.4k
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