Bioinfo_scripts

Misc scripts than can be useful for bioinformatics

Not all scripts were created by myself. Some have been adapted from scripts I have found. Credit can be found within each script

Not all scripts are ready to be used as is. They should be adapted for your needs.

snippets.sh

Miscellaneous one-liners for everyday use

collect_HISAT2_mapping_stats.sh

Collect HISAT2 mapping statistics from multiple summary files located in the current directory and organized them into a table

create_busco_plot.py

Create busco summary plot for several busco results as seen here https://busco.ezlab.org/busco_userguide.html#companion-scripts.

create_coverage_subset.R

Create coverage table for mafCoverage results

create_qualimap_summary.sh

Create summary table from qualimap results for several samples

ensembl_rapidrelease_homologue_query.py

Query the ensembl rapid release homologue gene page to identify homologues of a given list of genes

genestats.sh

Calculates several gene structure measures based on a GFF annotation file

get_assembly_stats.py

Get assembly statistics of a given fasta file

get_sniffles_summary.sh

Create summary table of Sniffles results

get_struct_var_vcf_subset.sh

Create summary table from svim and svim-asm results

makeAGPfromFasta.py

Create AGP file from a fasta file

misc_Rfucntions.R

Collection of reusable R functions

mummerplot_first30.sh

Create mummerplot of the first X chromosomes/scaffolds

mummerplot_top40.sh

Create mummerplot from list of chromosomes/scaffolds

plot_assoc.R

Generate manhattan plot from GWAS results

plot_interactive_pca.py

Create interactive PCA plot

plot_sample_mapping_summary.R

Plot histogram of mapping stats: mean coverage, mapping rate and mean mapping quality. Meant to work with the output of create_qualimap_summary.sh

plot_vcfstats_sample_summary.R

Plot histogram of num ref homozygous, num non ref hom, num heterozygous, ts/tv, indels from the bcftools stats output

qualimap_summary.sh

Get qualimap summary table

remove_duplicates_fasta.py

Finds duplicated sequences in a fasta file, keeps only one copy and combines the name of the duplicated scaffolds.

rename_fasta.py

Rename fasta sequences according to a two column file. First column is current name, second column is new name

reverse_complement_fasta.py

reverse complement the sequences in the fasta file whose names are in scaffs_to_convert.txt

RMout_to_bed.pl

Read a repeat masker output file and write TEs in a bed file

run_gwas_gemma.sh

Run and plot GWAS with Gemma: Run GEMMA Association Tests with Univariate Linear Mixed Models

Looking for signatures of selection

run_scan.sh and run_scan.

Convert data from input file to an object of class haploh.
Compute iHH, iES and inES over a whole chromosome

run_ihs.sh and run_ihs.R

Compute iHS (standardized ratio of iHH values of two alleles). Create manhattan plot with results

run_xpehh.sh and run_xpehh.R

Compute XP-EHH (standardized ratio of iES of two populations). Create manhattan plot with results

samplot_SV.sh

Plot SV larger than minsize from a SV vcf summary table

snakemake_rule.code-snippets

Visual Studio Code snippet to create snakemake rule

sniffles_var_summary.R

Get SV summary table from VCF with sniffles results

structural_var_summary.R

Get summary of the structural variants (from SVIM) found in a given vcf to stdout

vcf2eigenstrat.py

Convert a vcf file to eigenstrat format. Removes multi-alleleic and indel sites