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.