A group from Broad institute published a new de novo transcriptome assembly program in Nature Biotech. The paper came out in electronic version in April, and a collaborator of mine pointed it out to me. Until then, I was getting too frustrated with Velvet+Oases (especially Oases), because Oases was too demanding for RAM requirement. We have been using Trinity for transcriptome assembly since then, and I am so far happy with the results. Trinity seems to do the job with much less RAM.
I will post a comparison in my blog (http://www.homolog.us/blogs/) over the next few days and let you know here.
I will post a comparison in my blog (http://www.homolog.us/blogs/) over the next few days and let you know here.
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