Figure 1

Roche/454 read processing, decontamination, assembly and annotation. Raw Roche/454 reads were converted from sff to fastq format for editing and assembly. Relevant adapter sequences were trimmed, and reads failing to meet quality and complexity thresholds were removed. Reads that successfully map to rRNA, bacterial, human or host sequences were also eliminated. The remaining, high-quality, species-specific reads were assembled with Newbler’s cDNA specific protocol using our optimized parameter combination, translated using Prot4EST [44], and annotated using InterProScan [45, 46]. Statistical analyses can be carried out at the level of isotigs (unique transcripts) or isogroups (unique genetic loci) depending on the nature of the investigation.