Status Quo: Trinity Vs Oases

Question

[Biojl]

Hi,

I think there's been a while since the last version of oases came out. I was wondering what is the opinion of the people that routinely work on the novo transcriptomes assemblies in terms of quality, computational resources (RAM), documentation, etc.

I've found a comparison in terms of computational resources: http://www.homolog.us/blogs/2011/08/23/de-novo-transcriptome-assemblers-%E2%80%93-oases-trinity-etc-%E2%80%93-iii/

But for quality of the assembly I only have the results from the Oases papers (which favors oases). There is somebody who have tried the range of k-mer with trinity to make a fair comparison?

Thanks!

Answer 1

[Wrf]

As you say, there have not been many updates lately to Velvet/Oases, but there have been for Trinity. I have personally noticed better results with Trinity. Genes that were only partially assembled with Oases were fully assembled with Trinity.

This paper looks at particular genes for full-length reconstructions for phylogeny, and analyzes for chimeras. Oases doesn't perform so well. "Optimizing de novo assembly of short-read RNA-seq data for phylogenomics." http://www.ncbi.nlm.nih.gov/pubmed/23672450

Answer 2

[Biojl]

I found this paper recently: Comparative analysis of de novo transcriptome assembly

Answer 3

[keithforestdecker]

My personal experience (multiple plant and arthropod species with >150 million reads) is that Trinity performance is superior to Oases multi-k assemblies, in particular when judged based on highly accurate (>99% identity) assembly of known transcripts.

Trinity in-silico normalization is also indispensable for large data sets.

The active maintenance of the Trinity package is also a huge plus.

Answer 4

[Biojl]

Another player joins the competition. SOAPdenovo-trans

http://arxiv.org/abs/1305.6760