2.9 years ago by
Spain. Universidad de Córdoba
I have recently run an de novo assembly of a tree genome using 2X100 paired end data from Illumina using Trinity
I did it to find the ortholog of a tomato gen of interest in the tree I am working
I used Trinity using the regular adjustment of the program.
In the first assembly, I got over 860.000 fasta contigs files, and after running a local blast using the tomato sequence as the query, I could find several fasta candidates for my gen of interest. To my surprise, one of this contigs had an extension of DNA over 3700 bases encoding for a protein with more than 1100 amino acids and a degree of homology at the level of the protein higher than 67%. This makes me confident that Trinity is working much better that I was expecting
I run Trinity in the Galaxy web service of the Indiana University. The kindly provide me with free access to it, and I very much recommend it