Utilities

=========

2014-10-22

This repository contains various scripts and utilities that don't belong to any particular project.

Some of the code is quite useful as is while other code requires additional information to be useful. I'll try to update all pieces of code and example data files so that the code can be tested.

2023-07-24

Script	Purpose	Associated Projects
Ab1tofastq.py	Use BioPython to convert Sanger sequence files to FASTQ reads	Reuse of barley Sanger data
Alchemy_Calls.sh	Bash script to drive Alchemy genotype calls	Barley genotyping datasets

Name		Name	Last commit message	Last commit date
Latest commit History 186 Commits
LDheatmap		LDheatmap
coverage		coverage
genotype_conversion		genotype_conversion
notes		notes
randomized_rho		randomized_rho
rename_SNPs		rename_SNPs
splitter		splitter
.deepsource.toml		.deepsource.toml
.gitignore		.gitignore
Ab1tofastq.py		Ab1tofastq.py
Alchemy_Calls.sh		Alchemy_Calls.sh
FASTQ_dumper.sh		FASTQ_dumper.sh
Merge_BAMs.sh		Merge_BAMs.sh
README.md		README.md
SNPMeta.sh		SNPMeta.sh
SNP_Utils_BLAST.sh		SNP_Utils_BLAST.sh
SNP_replace.pl		SNP_replace.pl
SRA_download.sh		SRA_download.sh
Structure_replicates.sh		Structure_replicates.sh
VCF_From_FASTA.py		VCF_From_FASTA.py
accessions_names.pl		accessions_names.pl
ancestral_state.py		ancestral_state.py
ancestral_state_bed.sh		ancestral_state_bed.sh
archiver.py		archiver.py
bamtools_merge.sh		bamtools_merge.sh
blastn.sh		blastn.sh
blastone.sh		blastone.sh
bwa_mem.sh		bwa_mem.sh
calmMD.sh		calmMD.sh
class_population.sh		class_population.sh
coding_variant.sh		coding_variant.sh
count_derived.py		count_derived.py
count_derived.sh		count_derived.sh
count_derived_classic.py		count_derived_classic.py
coverage.sh		coverage.sh
derived_count.sh		derived_count.sh
ehnrho.sh		ehnrho.sh
file_rename.py		file_rename.py
frequency_class_population.sh		frequency_class_population.sh
genome_indexing.sh		genome_indexing.sh
getCol2.pl		getCol2.pl
list_unique.py		list_unique.py
make_index_bwa.sh		make_index_bwa.sh
makeblastdb.sh		makeblastdb.sh
minimap2.sh		minimap2.sh
minimap2_asm_syri.sh		minimap2_asm_syri.sh
minimap2_asm_vcf.sh		minimap2_asm_vcf.sh
mosdepth.sh		mosdepth.sh
mosdepth_exome.sh		mosdepth_exome.sh
paftools_call.sh		paftools_call.sh
phd_to_fastq.py		phd_to_fastq.py
private_SNPs_in_VCF.sh		private_SNPs_in_VCF.sh
read_numbers.sh		read_numbers.sh
samplot.sh		samplot.sh
samplot_BED.sh		samplot_BED.sh
samtools_sort.sh		samtools_sort.sh
seedms		seedms
select_samples.py		select_samples.py
smoove.sh		smoove.sh
sniffles.sh		sniffles.sh
subset_GFF.py		subset_GFF.py
svim-asm.sh		svim-asm.sh
tarchiver.py		tarchiver.py
tarchiver2.py		tarchiver2.py
variant_class.sh		variant_class.sh

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