Problems with de novo transcriptome assembly using 454 Titanium series

[ankitgupta.iitg]

Hi,

I am trying to do a de novo transcriptome assembly for a non-model organism using 454 GS FLX Titanium series. I have 656878 reads with average length of 377 base pairs which after cleaning, masking and assembling using TGICL (uses CAP3 to assemble), I have 87282 contigs and 317205 singletons. My contigs have an average length of 700 bp and an average coverage depth of 1.9.

I am afraid that the coverage is very low and am not getting enough contigs due to the large number of singletons. Any ideas on how can I improve my assembly? Are these problems inherent to the TGICL assembly program or should I use some other software like MIRA? Are there any other parameters that I should look at to give me a better idea about the quality of my contigs and assembly?

Thanks

[454Sequencing]

Hi ankitgupta.iitg,

If you've not heard previously, 454 Life Sciences will shortly launch a new transcriptome assembler as part of our next product update. I think you will find this new tool extremely useful in your de novo transcriptome assembly efforts. For more details please see the following:

http://www.454.com/applications/transcriptome-sequencing.asp

In the meantime, I'd recommend following up with your Roche representative. One of our bioinformatics Regional Applications Consultants should be able to lend a hand with your question.

Best regards,
Jason

Technical Product Manager
454 Life Sciences, A Roche Company