Alternative to CLC Genomics Workbench viewer

[k-gun12]

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!

[GenoMax]

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).

[k-gun12]

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.

[GenoMax]

Look into Geneious , if you are ok going commercial.

[gringer]

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.