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Question: Suggestions For De Novo Assembly Plant Transcriptome Without Reference
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gravatar for Jane Song
6.9 years ago by
Jane Song • 10
Jane Song • 10 wrote:
Dear Galaxy Expert, I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see at Galaxy web http://main.g2.bx.psu.edu/root . Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference. Many thanks and look forward to hearing back from you, Jane <galaxy-user@bx.psu.edu>
assembly • 1.3k views
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modified 6.9 years ago by David Matthews • 630 • written 6.9 years ago by Jane Song • 10
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gravatar for David Matthews
6.9 years ago by
David Matthews • 630
United Kingdom
David Matthews • 630 wrote:
Hi Jane, I have used Trinity on a local installation here at Bristol University. The main reason its not on Galaxy main is because its very very memory intensive (we run it on nodes with 256GB RAM). So you really need access to a big machine to run it. Having said all that the output is astoundingly good so it's worth the time and effort to get a run going if you can. Cheers David
ADD COMMENT • link written 6.9 years ago by David Matthews • 630
Baohua and Jane, As David noted, there is a Trinity wrapper for Galaxy, it works, and Trinity is great. However, Trinity is not enabled/installed on our public server (main.g2) or on Galaxy cloud instances (Amazon) right now. You'll need a little programming expertise to set up Trinity locally or on the cloud. Also, the Galaxy's team support for Trinity is very minimal right now as we haven't done much testing with it yet. Good luck, J.
ADD REPLY • link written 6.9 years ago by Jeremy Goecks • 2.2k
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