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
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
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