I have a largely undescribed species of a trematode parasite. It is similar
in life cycle to Schistosoma mansoni.
I have 454 and illumina single end reads from 4 different populations. I
need to first create a reference transcriptome.
The illumina data is... rough. I first assembled it using Trinity, and
found only 531 contigs... which is orders of magnitude less than I
expected.
So I used MIRA to do a 454 assembly, a illumina assembly and a hybrid
assembly. Now I'm trying to figure out which is any good.
MIRA Assembly Statistics
Platform
Reads
# Contigs
Max
Coverage
Average Quality
454
33779
1938
43505
45
Illumina
72276
3033
34767
43
Hybrid
454 and Illumina
98259
6726
77610
55
Obviously there are the most contigs in the hybrid assembly, but the
percentage of reads from each population that map to the reference is
significantly lower (~55% of reads from each population map to the
reference).
How could I improve this? I'm drowning a bit in the literature and any/all
help is welcome.
Thanks!
CJ
--
CJenkins, MS
PhD Candidate
Washington State University/University of Idaho
