What Programs Are There For Transcriptome Assembly?
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?
• 6,291 views
•
link
updated
by
Mikael Huss
•
written
by
Panos
•
written
by
Panos
1 answer
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:
• 186 views
•
link
written
by
Mikael Huss
Log in to answer this question.
More posts like this
-
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genom…
written by zizigolu
-
Denovo assembly or Reference based assembly for identifying novel lncRNAs
written by newbie
-
Should I be using the reference genome
written by Biogeek
-
having up-regulated and down-regulated isoforms in Trinity output
written by Whoknows
-
Whole exome sequencing de novo assembly
written by raphaelschneider •
-
How to get scaffold information from Trinity?
written by Paul
-
Futher analysis on Trinity fasta output
written by Whoknows
-
De Genes And Isoforms?
written by lzsph •
-
Select Contigs For Quantification After Assembly Of Rna-Seq Short Read Data?
written by Tianyang Li •
-
Tools For De Novo Transcriptome Assembly Of Ion Torrent Reads?
written by Ahdf-Lell-Kocks •
