Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.

ABSTRACT:

Background

RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity.

Method

Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta) was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs.

Result

To take advantage of increased read length of >150

SUBMITTER: Hara Y 

PROVIDER: S-EPMC4652379 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature