Question: Input needed to find the best metatranscriptome assembler
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gravatar for sentausa
3.5 years ago by
sentausa630
France
sentausa630 wrote:

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:

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!

 

ADD COMMENTlink modified 3.2 years ago by h.mon19k • written 3.5 years ago by sentausa630

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!

ADD REPLYlink written 8 months ago by steph_tf0
1

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

ADD REPLYlink written 8 months ago by sentausa630
0
gravatar for h.mon
3.2 years ago by
h.mon19k
Brazil
h.mon19k wrote:

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

ADD COMMENTlink written 3.2 years ago by h.mon19k

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

ADD REPLYlink written 3.2 years ago by sentausa630
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