assembly_stats.sh -i genome.fasta -n <num_of_chr> Creates len, syn, whitelist, renamelist stats files, taking into account number of chromosomes.

bwa_index.sh -i genome.fasta Creates a folder, softlinks to fasta in it, bwa index and goes back.

bowtie2_index.sh -i genome.fasta Creates a folder and in it a soft reference to fasta, bowtie2-build and goes back.

draw_coverage.sh Draws genomecov coverage.

draw_densities_of_hetero.sh Draws snps/indels coverage.

krater.sh -i <fastq_prefix> Fastq file prefix (file name without .final_[12].fastq). The rest of the default parameters are.

pseudosomal_region.sh -i <file *_10000_windows_stats name> -s <name of sex scaffold> Creates folder pseudosomal_region, moves transferred file with stats into it, creates new one with stats only by sex chromosome, starts Biocrutch/scripts/genomecov/pseudoautosomal_region.py

same_filtration_but_using_bcftools.sh -i <file.vcf> Run in the folder prepare_region_list. Will create the same_filtration_but_using_bcftools folder and do everything up to the homo/hetero files. Will run draw_densities_of_hetero.sh.

template.sh Template for creating new scripts.