Scripts for Alignment and Analysis of TLR sequences related to: "A novel bioinformatic approach to characterise toll-like receptor gene diversity in threatened birds," a master's thesis characterising TLR gene diversity in tūturuatu/shore plover (Thinornis novaeseelandiae), kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi), and kakī/black stilt (Himantopus novaezelandiae). Thesis Permanent Link: https://ir.canterbury.ac.nz/handle/10092/101832.
Associated Peer-reviewed Publications:
0_blast_tlr_search.sh Script to find TLR sequences within a species genome, using reference TLR sequences from related species
1_trimming.sh Script to trim raw fastq files and analyse them with fastqc prior to aligment
2_alignment_pipeline.sh Script to align trimmed fastq files to species reference genome
3_filtering.sh Script to filter population vcf file
4_haplotype_creation.sh Script to phase and create haplotypes for all individuals in the population vcf file