For species that lack reference genome sequences, or whose genomes are poorly annotated, de novo short-read transcriptome assembly may be a practical alternative to conventional expressed sequence tag–based approaches and to methods that depend on short-read alignments.
Researchers at Canada’s Michael Smith Genome Sciences Centre have developed a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis.
When de novo assembly is applied to short-read transcriptome data, longer assembled contigs, rather than reads, are aligned to a reference genome, and contig alignments can be compared to transcript annotations to identify new transcripts and new transcript structures. Such an approach has the advantage of requiring no prior knowledge of exon-exon junctions.
Trans-ABySS – can be accesses online at:
Robertson G, et al. (2010) De novo assembly and analysis of RNA-seq data. Nature Methods [Epub ahead of print]. [abstract]