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Old 02-17-2011, 12:31 AM   #1
pasta
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Question Geneious: Any good ?

Dear all,

Has any of you tried the Geneious software for Next-Gen sequence assembly or for other applications? Is it worth paying for a software that use 70% of non-commercial sofware in its suite?

Thank you for your feedback,

antoine
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Old 02-27-2011, 04:08 PM   #2
Milkman
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I use it for short read assembly on my desktop which has only 2 Gb ram. Very slow compared to Velvet but nice graphical outputs that I have used in publications and ppt presentations. It is easy to use on Mac and PC for someone like me who has no bioinformatics support to teach me how to assemble and annotate sequences.
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Old 02-27-2011, 11:38 PM   #3
pasta
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Thank you Milkman for your feedback
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Old 02-28-2011, 01:35 AM   #4
zee
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Nice graphics but only the Pro version accepts SAM/GFF/GFF3 format.

1. No jumping to position in contigs using coordinates
2. No support for BAM files
3. Slow to load large SAM files
4. Cannot view multiple tracks in 1 view

Better off using a free viewer for NGS like IGV, Tablet, Savant and many more.

Geneious is great for doing the basic sequence analysis, low throughput kind of work like drawing trees, BLASTing sequences, Clustalw. Not something I would spend money on.
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Old 02-28-2011, 09:21 PM   #5
Milkman
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Default Geneious

I use geneious pro for more than low throughput tasks such as alignments, trees etc, although it is good with them too. With Illumina data (78 nt reads) it will quite quicky do denovo assembly of 20 million reads then batch Blast the contigs in groups of 200. With reference assembly it is faster, of course. For someone without Perl/Unix experience, I recommend it. The free version is worth playing with until you can find the $400 for Pro.
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Old 03-01-2011, 07:30 PM   #6
zee
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FYI the next version of Geneious i.e 5.4 will support BAM files.
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Old 03-02-2011, 11:34 PM   #7
pasta
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Ok thank you all for your feedback. It seems that Geneious is more suitable for biologists than for bioinformaticians.

Thanks

antoine
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