Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler.
Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.
Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India.
Kiran Gopinath
KG
Bankar
Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India.
Vivek Nagaraj
VN
Todur
Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India.
Rohit Nandan
RN
Shukla
Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India.
Madavan
M
Vasudevan
De novo transcriptome assembly; Illumina; Trinity