Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.

ABSTRACT:

Background

Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes.

Results

A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads wit

SUBMITTER: Feldmeyer B 

PROVIDER: S-EPMC3128070 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature