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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 with median read length of 61 bases. The assemblies generated by  VELVET ,  OASES , and SeqMan  NGEN  differed in the total number of contigs, contig length, the number and quality of gene hits obtained by  BLAST  searches against various databases, and contig performance in the mt genome comparison. While  VELVET  produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in  BLAST  searches and the mt genome alignment. The best overall contig performance resulted from the  NGEN  assembly. It produced the second largest number of contigs, which on average were comparable to the  OASES  contigs but gave the highest number of gene hits in two out of four  BLAST  searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of  BLAST  hits.    Conclusion  Our results document the first  de novo  transcriptome assembly of a non-model species using Illumina sequencing data. We show that  de novo  transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology.

bmc genomics

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