Input needed to find the best metatranscriptome assembler

Question

[sentausa]

Hi everyone!

I'd like to choose an assembler for my eukaryotic metatranscriptomics HiSeq (2x100 bp) data from soil (the cDNAs are from eukaryotic poly-A mRNAs) and I saw these two papers:

• Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
• IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information

In these papers, the authors made a comparison of metatranscriptomic assemblers but they seem to have different conclusion on Trinity's performance. The first paper stated that Trinity "provided the best performance", but the second paper showed that Trinity has the highest error rate. So, could anyone here help me to decide whether I should use Trinity (or perhaps IDBA-MTP)?

Thanks!

[steph_tf]

Hi! I would like to know how you finally deicided to perform the assembly and annotation of your data, I'm working on something very similar, and until now I'm using only Trinity. best regards!

[sentausa]

Hi. Finally I used only Trinity, and I used MG-RAST for the annotation. Good luck!

Answer 1

[h.mon]

Use both assemblers, and evaluate the assemblies with transrate and, perhaps, percentage of annotated contigs as per the paper you listed.

[sentausa]

Thanks for mentioning transrate; it's an interesting tool.