Fig. 1

TC-hunter workflow and subprocesses. TC-hunter can be run with either fastq files (blue) or BAM files (green). * If fastq files are the input, the construct and host reference files are needed as well as the genomic annotation of the construct. ** If BAM files are the input, the alignment should be done against a joint genome (construct + host references), a genomic annotation file of the construct is also needed. Reads are depicted as red (forward reads) and blue rectangles (reverse reads), where a connecting line indicates both reads are paired. 1) The configuration file will dictate if fastq files are to be aligned to a composite reference genome (host genome + construct sequence). 2) TC-hunter extracts information about discordant read pairs (those where one read is aligned to the host and the other read is aligned to the construct) and 3) chimeric reads (those where a single read aligns to both the host and the construct). 4) Then, this information is used to detect the transgenic insertion region(s) and 5) to extract coverage data. 6) Next, TC-hunter determines the break point location of the transgenic insertion site and ranks the results according to coverage evidence. Finally, it generates visualization aids and a summary report 7) for further evaluation of the results