This repository contains the scripts used for processing data in the following paper:
Rapid evolution driven by translocation-associated Non-Mendelian unequal segregation
- R (v4.3.3)
- Trimmomatic (v0.39)
- GATK (v4.3.0.0)
- bwa (v0.7.17-r1198-dirty)
- samtools (v1.13)
- bcftools (v1.19)
- Flye (v2.9.5)
- Medaka (v2.0.1)
- NextPolish (v1.4.1)
- Ragout (v2.3)
Script_for_parental_strains.sh is used for processing NGS sequencing data of parental strains to produce alignment file (BAM) and variant file (VCF).
Markers_define.R is used for defining the SNP markers between two parental strains from vcf files.
Script_for_hybrid_samples.sh is used for processing NGS sequencing data of hybrid samples to produce alignment file (BAM), variant file (pileup) and SNP markers.
Extract_downstream_data.R is used for extract hybrid sample variant data as csv files from pileup files and parental SNP markers for downstream analysis.
Genome_assembly_and_polishing.sh is used for genome assembly, polishing and scaffolding using TGS and NGS data of parental strains.