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Alternatives To Newbler To Assemble Ion Torrent Reads?

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

assembly ion-torrent
• 5,602 views • link
updated by JC JC • written by 14134125465346445 14134125465346445

2 answers

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.

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written by Arpitha Hebbar Arpitha Hebbar

I have been using SPAdes without problems.

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updated by Ram Ram • written by JC JC

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?

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written by Adam Witney • Adam Witney

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.

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updated by Ram Ram • written by 5heikki 5heikki

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