This was performed using the SAM files from BWA and custom-made Perl scripts (File S1).
In addition, a custom Perl script was used to obtain gene annotations from Biomart, and a custom python script was used to count the tags in each Ensembl gene using the sam output files from bowtie.
The Cuffdiff algorithm then re-estimated the abundance of transcripts listed in the GTF file using alignments from the SAM file, and concurrently tested for differential expression between the high γ-decalactone and the no γ-decalactone pools using a rigorous statistical analysis [ 28].
Velvet Columbus module [ 27] was used to perform a reference guided de-novo assembly in which the SAM file was used to assign reads into their positions.
The software program readingExtension was used to extend the reads of the SAM file from approximately 51 to 400 nt (Additional file 3: TomatoProgramCode zip file).
The SAM file produced by Bowtie was processed using SAM tools (Li et al. 2009) to obtain the mean coverage of the positions covered by reads.
The average depth of coverage of the mapped sites was estimated from the SAM file and was used to determine the coverage cut-off of the SNP calling.
Alignment of the SAM file and removal of duplicated reads were conducted using Picard (http://picard.sourceforge.net) and SAMtools [ 31].
The mapping quality in the SAM file did not present a sufficient value for the use as threshold.
The SAM file generated by BWA was then converted to BAM and the reads were sorted by chromosome using samtools [ 23].
