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TC-hunter searches for transgenic insertion sites in a host genome and returns figures and a report to support these findings.
There's two programs; TC_hunter and TC_hunter_BWA.
- 🟩 TC_hunter.nf
Accepts one or several aligned BAM files (mapped to both host and transgenic sequence) as input. TC-hunter then identifies anchors and chimeric reads that maps to both host and transgenig sequence.
- 🟨 TC_hunter_BWA.nf
TC_hunter_BWA accepts raw pair end fastq files (from one or several samples) as input and performes BWA MEM alignment before searching for trasgenic insertion site.
