Additional shell scripts to screen data via bash or executing single programs.
- clean_genomes.sh: usefull for filtering clean genomes from sourmash.
- snippy_loop.sh: loop for automatic snippy analysis for multiple fastas. Comparison against illumina fasta.
- snippy_loop_for_heatmap.sh: runs snippy for all files in ctgs and reference directory and made an .csv for heatmap plotting (ref;ctgs;SNPs)
- snippy-multi_tab.sh: build a .tab file from samples for snippy-multi
- samtools_longest.contig: get longest contig from multi-fasta file.
- contig_count.sh: Print number of contig of each sample.
- ill_clean_samples.sh: Extracting only mapped contigs.
- ont_clean_sample.sh: Extracting only longest contig (Chromosom)
- make_directorys.sh: make directorys from filenames
- renaming_vcf.sh: renaming files inside a directory after the directory name
Useful and tested code blocks for multiple programs. Could be used for further pipelines.