A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

ABSTRACT: For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1) assessing the performance of three different assembly tools (2) using both single and multiple k-mer (MK) approaches (3) examining the influence of the number of reads used in the assembly (4) merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck). We find that taking

SUBMITTER: Moreton J 

PROVIDER: S-EPMC4070175 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature