Question

Alternatives To Newbler To Assemble Ion Torrent Reads?

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11.5 years ago

14134125465346445 ★ 3.6k

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

assembly ion-torrent • 4.8k views

ADD COMMENT • link updated 10.5 years ago by JC 13k • written 11.5 years ago by 14134125465346445 ★ 3.6k

score 5 · Answer 1 · 2013-05-20

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.

Ram · Answer 2 · 2014-06-02

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10.5 years ago

JC 13k

I have been using SPAdes without problems.

ADD COMMENT • link updated 4.9 years ago by Ram 44k • written 10.5 years ago by JC 13k

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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 REPLY • link 10.4 years ago by Adam Witney ▴ 10

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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 REPLY • link updated 4.9 years ago by Ram 44k • written 8.8 years ago by 5heikki 11k