1. Qualuty control (trimomatic)

2. Reference genome alignmnet (bwa)

3. Alignment file convertion (optional) (samtools)

4. Output vcf file (bcftools)

ps : vcf (variant calling file)

1. check_snp_position : This perl is checking mutation position with "gff file" from NCBI

perl check_snp_position.pl sample.gff sample.vcf 

2. merge_annotation (need to formating uniport annotation file before this step)

perl merge_annotation.pl HOL1_variantion_all.txt uniprot_annotation_info.txt > cds_merged.txt 

3. coding_or_not : This perl is split coding sequece mutation and non-coding sequece mutation

perl coding_or_not.pl cds_merged.txt

4. noncoding_analysis : This perl is checking the nearest cds of non-coding mutation

perl noncoding_analysis.pl sample.gff mutation_in_non-coding_region.txt

5. check_aa_sequence : This perl is primary check amino acid mutation with DNA sequence translation to amino acid sequence

perl check_aa_sequence.pl ATCC824_genome.fna codon_transfer.txt mutation_in_coding_region.txt 

6. aa_forword_check :

perl aa_forword_check.pl amino_acid_primary_check.txt mutation_cds.faa mutation_cds_modified.faa mutation_in_coding_region.txt 

7. 
perl cds_cross_check_v2.pl 0_S4_L001_final_report.txt 1_S5_L001_final_report.txt  2_S6_L001_final_report.txt