DE NOVO TRANSCRIPTOME ASSEMBLY OF SOLID SEQUENCING DATA IN CUCUMIS MELO

Purru Supriya 1 and K V Bhat 2

1 Division of Bioinformatics, Indian Agricultural Research Institute, Pusa campus, New Delhi 110012, India

aarush.supriya@gmail.com

2 National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India

kvbhat@nbpgr.ernet.in

ABSTRACT

As sequencing technologies progress, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. In the present study, we have carried out a comparison of two assemblers (SeqMan and CLC) for transcriptome assembly, using a new dataset from Cucumis melo. Between two assemblers SeqMan generated an excess of small, redundant contigs where as CLC generated the least redundant assembly. Since different assemblers use different algorithms to build contigs, we followed the merging of assemblies by CAP3 and found that the merged assembly is better than individual assemblies and more consistent in the number and size of contigs. Combining the assemblies from different programs gave a more credible final product, and therefore this approach is recommended for quantitative output.

KEYWORDS

De novo assembly, Transcriptome, Contig, RNA-Seq

For other details : https://airccse.com/bioej/papers/2115bioej02.pdf