Flow diagram of the assembly procedure. Female and male normalized pools of cDNA were sequenced separately using Roche 454 GS-FLX Titanium chemistries. NEWBLER was initially used to assemble the cleaned reads into contigs that could be classified into three categories based on the sex-of-origin of the reads: Female Contigs (FC, contigs made only from female reads); Male Contigs (MC, made only from male reads); Both Contigs (BC, contigs made from both male and female reads). The remaining male and female singletons went through additional assembly using MIRA. After each assembly process an attempt was made to map the remaining singletons to the contigs using Blast. The contigs and singletons were clustered based on homology in the HomoloGene database or to the Ensemble annotated gene models from the Anolis lizard draft genome (AnoCar1.0). The NEWBLER contigs were put into graph-clusters based how reads were split and assigned to different contigs during the NEWBLER assembly process (see Additional file 3 for full description). In the graph-clusters the contigs (nodes) are linked by reads (edges) that were split between the contigs.
Schwartz et al. BMC Genomics 2010 11:694 doi:10.1186/1471-2164-11-694