Lactuca sativa. Lactuca sativa

High quality sequences were extracted from the primary output of the Illumina sequence analysis pipeline (qseq files) prior to assembly. The parser analyzed quality scores in qseq files and trimmed everything after the first failed score, 'B'. Upon trimming, sequences longer than 40 nt and those with a GC content within the 20 to 80% were selected for the assembly. High quality selected reads (~80 million) of the normalized mRNA-Seq library SRP004854 were assembled using Velvet with different K-mer values (35 to 55) and CLC Genomic Workbench. Contigs generated by Velvet and CLC were combined into a mega-assembly using CAP3. The final assembly was validated by re-alignment of the raw reads to the consensus sequences.