What Programs Are There For Transcriptome Assembly?

Question

[Panos]

I know about the Trinity package which is good for de novo reconstruction but is there anything else?

What about programs that do mapping of RNA seq data against a reference genome?

Answer 1

[Mikael Huss]

Transcriptome assembly software can (as you suggest in your question) be divided into de novo assemblers and reference-guided assemblers.

For de novo assembly, there is e g:

• Trinity (as you wrote)
• Velvet followed by Oases
• TransAbyss

and probably many others.

For reference-guided assembly (or "transcriptome reconstruction" as the developers of Scripture call it) there is e g:

• Cufflinks
• Scripture