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Old 02-01-2018, 06:54 AM   #1
k-gun12
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Default Alternative to CLC Genomics Workbench viewer

Qiagen has hiked the pricing and changed the licensing terms of the CLC software line to the point that I can no longer afford it after a decade of use. What I found myself using particularly in the later years was the viewer; it was useful for viewing, scrolling and annotating short-read and spliced alignments based on the mapping, piecing together gene structures, finding splice sites, polymorphisms, etc. I've tried IGV but found it a little clunky.. are there any other decent alternatives out there?

Thanks!
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Old 02-01-2018, 08:35 AM   #2
GenoMax
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Sounds like you are/were a power CLC user. When you have used a program for a decade anything else you try is going to feel ... different. Following examples are more or less pure viewers.

IGB (http://bioviz.org/igb/), Tablet (https://ics.hutton.ac.uk/tablet/) are a couple of other options. Golden helix (an otherwise commercial software) has a genome browser available for free (http://goldenhelix.com/products/GenomeBrowse/index.html).
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Old 02-01-2018, 08:46 AM   #3
k-gun12
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Thanks. I'll check those out. I don't mind going commercial again, but the way Qiagen treated existing CLC customers as a cash cow after buying the company was pretty bad.
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Old 02-01-2018, 09:43 AM   #4
GenoMax
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Look into Geneious , if you are ok going commercial.
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Old 02-03-2018, 11:57 AM   #5
gringer
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Quote:
Originally Posted by k-gun12 View Post
the way Qiagen treated existing CLC customers as a cash cow after buying the company was pretty bad.
My probably-biased point of view (as a bioinformatician) is that even with the original CLC prices, a company would get more benefit out of hiring a dedicated bioinformatician than paying for CLC.

Someone needs to interpret the results produced by CLC, and the skill/training gap between result interpretation and result generation from [much] cheaper software is quite small. If a bit of hand-holding is needed, I'd recommend Geneious because it has a much more open community and plugin system.
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alignment, bioinformatics, genome viewer, read mapping

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