giraffe-tes | Discover TEs in low-coverage giraffe genomes

Giraffe TEs is a Shell library. Giraffe TEs has no bugs, it has no vulnerabilities and it has low support. You can download it from GitLab.

giraffes are a relatively young group of mammals with [four recognized species] that diverged [around 28 mya] northern giraffe (g. camelopardalis), southern giraffe (g. giraffa), reticulated giraffe (g. reticulata), and masai giraffe (g. tippelskirchi). the genome of one giraffe species has been [analysed to find clues to its unique morphology] however, no attention has been paid to mobile genetic elements (meis), also termed transposable elements (tes). we used the kordofan giraffe genome assembly as a reference to map de-novo sequenced low-coverage genomic data using bwa mem (todo cite). to identify te insertions based on discordant reads, we used the [mobile element locator tool (melt)] to identify te insertions in the giraffe genomes. code: scripts and programs used in the analysis. especially important are the run-melt-phase-[1-4] as well as the run-melt-pipeline-complete scripts. also the pca.r script that computes pcas. data: clean: cleaned data ready for analysis. this comprises mainly the te consensus sequences used for melt. raw: astral.tree: tree computed by raphael with astral consensi: raw te consensus sequences, with unclean headers and possible ambiguities genetic_distance.tree: giraffe tree computed by raphael using ml and genetic distances genomes: reference: the kordofan giraffe reference genome: assembly (fasta format, with index) and repeatmasker annotation (bed format) samples: mapped reads from each of the giraffe individuals in bam format, along with