ABSTRACT
More recently, the ease of sample preparation and low cost of short-read transcript sequencing (e.g., Illumina RNA-Seq) have made it possible to e¤ectively reveal the transcriptome of any organism. ™e depth of coverage obtained through RNA-Seq data has greatly enhanced prokaryotic and eukaryotic transcriptomics, demonstrating that loci are di¤erentially expressed and in the case of eukaryotes can be alternatively spliced far beyond what was known from the results obtained by the generation of ESTs. Short reads can be assembled into transcripts using computationally intensive so©ware such as ALLPATHs (Butler et al., 2008), PEACE (Rao et al., 2010), Trans-ABySS (Robertson et al., 2010), or SOAPdenovo (soap. genomics.org.cn) and Velvet/Oases (Zerbino and Birney, 2008) assembly packages. Although some of these packages were originally designed for genomic assembly, they have been enhanced to deal with the variable read coverage of transcriptomes (which is generally not an issue in shotgun genome sequencing), as described next.
